The South China Sea is a crucial habitat and potential nursery for cetaceans. This study involved five ship-based visual surveys in three summers and two springs from 2020 to 2023, combined with environmental DNA (eDNA) metabarcoding, an emerging tool, to understand the relative abundance and spatial and temporal distribution of cetaceans in offshore and abyssal areas of the South China Sea. The combination of visual observations and eDNA metabarcoding enabled the detection of a total of 18 cetacean species, and 12 species were identified by both methods. Cetaceans showed temporal variation; 7 species in the springs, and 17 species in the summers. Expedition route design, meteorological conditions, and sea conditions between the two seasons can partly explain the seasonal differences. The Hyperoodontidae and Physeteridae species tend to occupy regions with high bathymetric drop gradients, particularly those situated on continental slopes and seamounts. The Delphinidae species are more widely distributed and relatively abundant. Of the cetaceans successfully amplified by eDNA metabarcoding, species with larger group sizes and closer distances tend to be more easily detected. Although the complex and turbulent hydrographic environment of the oceans reduces the duration of eDNA and increases the uncertainty in capturing eDNA signals, our findings indicate that eDNA techniques can provide additional information and hold promise as a potential complementary tool for cetacean monitoring.