Natural gas hydrates have received widespread attention due to their enormous resource potential, but previous researches have focused mostly on the passive continental margin in the northern South China Sea, while rarely on the active continental margin in the eastern South China Sea. Based on the analysis of multi-channel seismic profiles in the active continental margin area of the Manila Trench in northeast of the South China Sea, this paper identified typical gas hydrate indicators such as bottom simulating reflector, blanking zone, polarity-reversal, and fluid migration channels, such as reverse fault and mud diapir are identified in this paper. The Orogenic Belt in southwestern Taiwan is an extension of the accretionary wedge of the Manila Trench. The associated gas of mud volcano is mainly CH₄ and minorly showing high nitrogen anomaly. The geochemical characteristics of the associated gas show that natural gas in this area is mainly mature hydrocarbon gas of pyrolysis origin, and is mainly the contribution of Neogene thick marine sedimentary source rock. According to the analysis, the cause is that the plate subduction brought deep hydrocarbon into the accretionary wedge and formed a high-pressure environment. The thermally generated hydrocarbon gas migrated upward along mud diapir and reverse fault. During the migration, some natural gas was gradually transformed by decomposition of microorganisms and mixed with in-situ microbial gas. The thermogenic and biogenic methane eventually mixed in the suitable stable zone to form a mixed gas hydrate reservoir dominated by thermogenic and partly biogenic. In addition, with the change of external environment and the continuous activities of subduction movement, the stability of natural gas hydrate is damaged and decomposition leakage occurs, which may cause landslide. In the further exploration and development of natural gas hydrate resources in this area, we must pay attention to the potential geological disaster risk.