Abstract: The non-invasive and easy-to-implement photo-identification technique has been widely adopted in cetacean research worldwide. While its application has led to significant progress in studies on population dynamics, social behavior, and conservation biology of the Indo-Pacific humpback dolphin (Sousa chinensis) in China, its use for offshore and deep-sea cetaceans remains highly limited. On the basis of over 200000 images collected during seven multi-objective vessel-based surveys conducted in the South China Sea from 2019 to 2024, this study built a photo-identification catalog for 11 cetacean species and Ziphiidae using exclusively natural distinguishable features. 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.