The diel vertical migration (DVM) of plankton and nekton plays an important role in the energy flow and material cycling of marine ecosystems. Especially in shelf seas, seasonal environmental variations may distinguish DVM characteristics in winter mixed water from summer pattern. Therefore, to investigate the patterns and influencing factors of winter DVM in East China Shelf Seas (ECSS), we carried out comprehensive research based on high‐resolution multi‐frequency acoustic data during the winter of 2019/2020. The results showed that: (a) acoustic and zooplankton sampling data can effectively capture the widely existence of winter DVM of different biological community in ECSS and their spatio‐temporal variabilities. (b) In East China Sea, the migration was mainly dominated by the Gas‐bearing class (GB), which had fast migration speed, compared to the Yellow Sea where the migration was dominated by the Fluid‐like class (FL). In addition, GB descends earlier than FL. (c) For large scale factors, during the full moon, the GB will aggregate deeper and the FL shallower, compared to the new moon, and regional temperature is an important factor affecting the distribution of organisms at meridional direction; for small scale processes, cold and warm currents and ocean fronts can also affect migration behavior. In the muddy area with full moon and spring tide, GB and FL show different inconsistent migration compared to normal relatively consistent pattern. These results will help us to better understand the physiological, ecological and environmental elements that control winter DVM, facilitating the management of ecosystem‐based fisheries resources.