Abstract: This study is based on over 200000 images collected during seven multi-objective vessel-based surveys conducted in the South China Sea from 2019 to 2024. We built a photo-identification catalog for 11 cetacean species and the family Ziphiidae using natural marks as distinguishable features. The study evaluated the applicability of photo-identification techniques for cetacean population research in the South China Sea and the feasibility of using existing visual survey data for capture-recapture analysis. Our results indicate that: (1) most cetacean species in the South China Sea can be identified using natural marks, though the marked individual ratio over the population varies substantially across species; (2) the cumulative discovery curves of all species are still raising, suggesting incomplete population coverage, and their step-like growth suggests that detection is influenced by animal behavior, survey design, and effort; (3) among 12 photo-identification catalog, only short-finned pilot whales (Globicephala macrorhynchus) exhibited re-sightings (re-sighting rate: 4.8%). POPAN model analysis suggested a population size of approximately 8148 individuals (S.E.: 4796, 95% CI: 2798—23730) in the South China Sea. These findings show that photo-identification holds considerable potential for population biology studies of medium- to large-sized cetaceans with relatively small population. By optimizing survey design and increasing sampling effort, further data on population dynamics and social structure can be obtained, thereby providing a scientific basis for cetacean management and conservation of the region.