Intense fishing pressure and climate change are major threats to coastal fisheries. Larimichthys crocea (large yellow croaker) is a long-lived fish, which performs seasonal migrations from its spawning and nursery grounds along the coast of the East China Sea (ECS) to overwintering grounds offshore. This study used length-based analysis and habitat suitability index (HSI) model to evaluate current life-history parameters and overwintering habitat suitability of L. crocea, respectively. We compared both life-history parameters and overwintering HSI between recent (2019) and historical (between 1971 to 1982) to analyze the fishing pressure and climate change effects on the overall population and overwintering phase of L. crocea. In the context of overfishing, the length-based analysis indicated serious overfishing of L. crocea, characterized by reduced catch yield, size truncation, constrained distribution, and advanced maturation in the ECS, namely recruitment bottleneck. In the context of climate change, the overwintering HSI modeling results indicated that climate change has led to decreased sea surface temperature during L. crocea overwintering phase over the last half-century, which in turn led to area decrease and an offshore-oriented shifting of optimal overwintering habitat. The fishing-caused size truncation may constrain the migratory ability and distribution of L. crocea, subsequently led to the mismatch of the optimal overwintering habitat against climate change background, namely habitat bottleneck. Hence, while heavily fishing was the major cause of L. crocea fishery collapse, climate-induced overwintering habitat suitability may have intensified the fishery collapse of L. crocea population. It is important for management to take both overfishing and climate change issues into consideration when developing stock enhancement activities and policy regulations, particularly for migratory long-lived fish that share a similar life history to L. crocea. Combined with China’s current restocking and stock enhancement initiatives, we propose recommendations for future restocking of L. crocea in China.