The South China Sea (SCS) is vital habitat and potential nursery and feeding grounds for large cetaceans, such as the sperm whale (Physeter macrocephalus), making understanding of the temporal and spatial patterns of cetaceans in this region essential. We examined the accuracy of environmental DNA (eDNA) in detecting cetacean species diversity and determine the spatial and temporal distribution of cetaceans in the northern SCS. We conducted 5 ship‐based visual surveys for cetaceans in 3 summers and 2 springs from 2020 to 2023 and used eDNA metabarcoding to determine the relative abundance and spatial and temporal distribution of cetaceans in offshore and abyssal areas of the northern SCS. We detected 18 cetacean species through visual observations and eDNA metabarcoding. Both methods identified 12 species in common. Cetaceans’ presence varied temporally. We detected 7 species in the springs and 17 species in the summers. Expedition route design, meteorological conditions, and sea conditions between the 2 seasons partly explained the seasonal differences. The species of Ziphiidae, Physeteridae, and Kogiidae tended to occupy regions with high bathymetric drop gradients, particularly those situated on continental slopes and seamounts. The Delphinidae were more widely distributed and relatively more abundant. Of the cetaceans successfully identified by eDNA metabarcoding, species with relatively large group sizes and that were relatively close to the sampling sites tended to be more easily detected. Our results provide new information on the relative abundance and spatial and temporal distribution of cetaceans and indicate that eDNA techniques can provide additional information and serve as a complementary tool for cetacean monitoring and conservation.