The Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (IVPP), traces its origins to the Cenozoic Research Laboratory of the Geological Survey of the Ministry of Agriculture and Commerce, which was established in Beijing on April 19, 1929, and was primarily tasked with excavating and studying fossils from the Zhoukoudian Peking Man site.

On December 2, 1929, Pei Wenchung discovered the first skull of Peking Man at Zhoukoudian, establishing Homo erectus as a defined stage of human evolution. By 1937, the site had yielded remains of about 40 individual specimens, including five complete skulls, along with abundant animal fossils. In addition to his work at Zhoukoudian, Young Chungchien surveyed key vertebrate fossil localities across northern China and built the stratigraphic framework for the late Cenozoic in the region. When the War of Resistance against Japanese Aggression broke out, excavations at Zhoukoudian were halted, but Pei and Teilhard de Chardin continued their research in Beijing, while Young moved to Yunnan, where he conducted nearly eight years of fieldwork on Mesozoic dinosaur faunas in Lufeng and other areas. After the war, the laboratory was relocated to Nanjing.

Following the founding of the People's Republic of China in 1949, excavations at Zhoukoudian resumed. In 1951, the Institute of Paleontology of the Chinese Academy of Sciences(CAS) was formally established in Nanjing, with the Cenozoic and Vertebrate Paleontology Section as one of its units. In 1953, the Laboratory of Vertebrate Paleontology of the Chinese Academy of Sciences was officially founded in Beijing, becoming the first independent institution in China dedicated to vertebrate paleontology and paleoanthropology. In 1955, the first Academic Board was formed, and Young Chungchien proposed the research priorities of "two deposits" and "four origins," along with the goals of "filling three gaps" and "accomplishing three wishes." In March 1957, the journal Vertebrata PalAsiatica was first published; in September of the same year, the Laboratory was renamed the Institute of Vertebrate Paleontology, Chinese Academy of Sciences. On April 11, 1960, the Institute received its current designation—the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (IVPP)—with Young Chungchien as its first director. In 1959, the Institute launched its first major international collaborative project, the Sino-Soviet Paleontological Expedition.

During the 1960s and 1970s, the Institute continued its scholarly pursuits. In 1966, the sixth Peking Man skull was discovered at Zhoukoudian. Fieldwork resumed in 1970, with surveys carried out in several southern provinces. In 1972, China's first popular science periodical Fossils was launched. In 1976, the Nanxiong conference on Cretaceous–early Tertiary red deposits revealed a significant Paleocene mammalian fauna, which was then among the most important early Paleocene faunas found outside North America.

After the reform and opening‑up, the Institute entered a new phase of vigorous growth. Acta Anthropologica Sinica, a quarterly academic journal, began publication in 1982; the Chinese Society of Vertebrate Paleontology was founded in 1984; the China–Canada Dinosaur Expedition Project—one of the largest and most productive international paleontological ventures of the 20th century—was launched in 1986. In the same year, the Institute was authorized to offer doctoral degrees, followed by the establishment of a postdoctoral research station in 1991. In 1994, the Paleozoological Museum of China opened to the public. In 1997, the IVPP initiated large‑scale field surveys and excavations in western Liaoning; the sustained efforts over the following years resulted in a series of major discoveries, including the Jehol Biota, which has been hailed by the international academic community as one of the most significant paleontological achievements of the 20th century.

Entering the 21st century, the IVPP joined the second and third phases of the CAS Knowledge Innovation Project, defining three major research directions—vertebrate evolutionary biology, vertebrate evolution and paleoenvironment, and paleoanthropology—and formulating two long‑term scientific programs: "Earth Environment and Life Processes" and "Global Change and Cultural Development." In 2008 and 2009, respectively, the Key Laboratory of Evolutionary Systematics of Vertebrates and the Joint Laboratory of Human Evolution and Scientific Archaeology were established; these were merged in 2013 to become the Key Laboratory of Vertebrate Evolution and Human Origins of CAS. In 2019, the IVPP was approved as one of the first group of training units for the discipline authorized to offer a degree program in archaeology at the University of the Chinese Academy of Sciences, and was also designated a key research base for "Survival and Evolution of Paleolithic Humans" by the State Administration of Cultural Heritage of China. In 2024, the quarterly journal Prehistoric Archaeology was launched.