The earliest records of the Peinan Site were made by Ryuzo Torii, an anthropologist in the early period of the Japanese Occupation in Taiwan. During his four visits to Taiwan for anthropological research, he took two photos of the stone pillars on the ground surface at the Peinan Site; the photos were probably taken in 1896. Tadao Shicano was the first scholar who studied the Peinan Site as an archaeological site. He mentioned in his published article in 1930 that there were numerous slate pillars erected on the ground surface. Shicano, from the legends that were told in the neighboring area of Peinan, inferred that there used to be an ancient tribe, and that the pillars were the remnants of their houses. During the 50 years of Japanese Occupation, the focus of researches had been on the remains of the erected stones on the ground. It was only in 1945 that Joubu Kanasaki and Naokazu Kokubun started carrying out excavations around the largest erected stones, and discovered the underground remains of pottery and houses.
Although there were quite a lot of researches conducted on the Peinan Site by native scholars in Taiwan after the Japanese Occupation Period, there were no excavations done. The Peinan Site was listed as a local heritage site by the Taitung County Government in 1975 and was upgraded to a Class III site in Taiwan in 1979. However, the job of historical preservation had still not been completed. The remains buried underground for thousands of years were unearthed, yet severely damaged during the construction of the Peinan New South Link Railway Station (today's Taitung Station) which began in 1980, and great interest was shown by the public. The Taitung County Government then invited Anthropology Professors Wen-hsun Sung and Chao-mei Lien from the National Taiwan University to lead the archaeological preservation project. There were 13 stages in the project, which was carried out over nine years. The results were impressive. New records of excavation were set in the archaeology history of Taiwan, namely the number of slate coffins and remains excavated. Among the unearthed artifacts, the public was especially in awe of the huge number of exquisite jade objects. The Peinan Site is undoubtedly one of the prehistoric sites that best represent Taiwan.