According to the Samguk Yusa, the nine-story wooden pagoda at Hwangnyongsa Temple was built by a Baekje artisan named Abiji in 645. Until the temple was burnt down completely during the Mongol invasion of Korea in 1238, it was the greatest symbol of the spiritual culture of the Korean people at that time and played an important role in the development of Buddhist thought in the country for about 700 years. At present, the only remaining features of Hwangnyongsa Temple, which is now in ruins, are the pagoda's stylobate and several foundation stones. In the past, many researchers made diverse inferences concerning the restoration of the original structure and the overall architecture of the wooden pagoda at Hwangnyongsa Temple, based on written records and excavation data. However, this information, together with the remaining external structure of the pagoda site and the assumption that it was a simple wooden structure, actually suggest that it was a rectangular-shaped nine-story pagoda. It is assumed that such ideas were suggested at a time when there was a lack of relevant data and limited knowledge on the subject, as well as insufficient information about the technical lineage of the wooden pagoda at Hwangnyongsa Temple; therefore, these ideas should be revised in respect of the discovery of new data and an improved level of awareness about the structural features of large ancient Buddhist pagodas. This study focused on the necessity of raising awareness of the lineage and structure of the wooden pagoda at Hwangnyongsa Temple and gaining a broader understanding of the structural system of ancient Buddhist pagodas in East Asia. The study is based on a reanalysis of data about the site of the wooden pagoda obtained through research on the restoration of Hwangnyongsa Temple, which has been ongoing since 2005. It is estimated that the wooden pagoda underwent at least two large-scale repairs between the Unified Silla and Goryeo periods, during which the size of the stylobate and the floor plan were changed and, accordingly, the upper structure was modified to a significant degree. Judging by the features discovered during excavation and investigation, traces relating to the nine-story wooden pagoda built during the Three Kingdoms Period include the earth on which the stylobate was built and the central pillar's supporting stone, which had been reinstalled using the rammed earth technique, as well as other foundation stones and stylobate stone materials that most probably date back to the ninth century or earlier. It seems that the foundation stones and stylobate stone materials were new when the reliquaries were enshrined again in the pagoda after the Unified Silla period, so the first story and upper structure would have been of a markedly different size to those of the original wooden pagoda. In addition, during the Goryeo period, these foundation stones were rearranged, and the cover stone was newly installed; therefore, the pagoda would seem to have undergone significant changes in size and structure compared to previous periods. Consequently, the actual structure of the original wooden pagoda at Hwangnyongsa Temple should be understood in terms of the changes in large Buddhist pagodas built in East Asia at that time, and the technical lineage should start with the large Buddhist pagodas of the Baekje dynasty, which were influenced by the Northern dynasty of China. Furthermore, based on the archeological data obtained from the analysis of the images of the nine-story rock-carved pagoda depicted on the Rock-carved Buddhas in Tapgok Valley at Namsan Mountain in Gyeongju, and the gilt-bronze rail fragments excavated from the lecture hall at the site of Hwangnyongsa Temple, the wooden pagoda would appear to have originally been an octagonal nine-story pagoda with a dual structure, rather than a simple rectangular wooden structure.