Identifying the spatio-temporal distribution hotspots of fishes and allocating priority conservation areas could facilitate the spatial planning and efficient management. As a flagship commercial fishery species, Largehead hairtail (Trichiurus japonicus) has been over-exploited since the early 2000s. Therefore, the spatio-temporal management of largehead hairtail nursery grounds could effective help its recovery. This study aims to predict juvenile largehead hairtail distribution patterns and identify priority conservation areas for nursery grounds. A two-stage hierarchical Bayesian spatio-temporal model was applied on independent scientific survey data (Catch per unit effort, CPUE) and geographic/physical variables (Depth, Distance to the coast, Sea bottom temperature, Dissolved oxygen concentration and Net primary production) to analyze the probability of occurrence and abundance distribution of juvenile largehead hairtail. We assessed the importance of each variable for explaining the occurrence and abundance. Using persistence index, we measured the robustness of hotspots and identified persistent hotspots for priority conservation areas. Selected models showed good predictive capacity on occurrence probability (AUC = 0.81) and abundance distribution (r = 0.89) of juvenile largehead hairtail. Dissolved oxygen, net primary production, and sea bottom temperature significantly affected the probability of occurrence, while distance to the coast also affected the abundance distribution. Three stable nursery grounds were identified in Zhejiang inshore waters, the largest one was located on the east margin of the East China Sea hairtail national aquatic germplasm resources conservation zones (TCZ), suggesting that the core area of nursery grounds occurs outside the protected areas. Therefore, recognition of these sites and their associated geographic/oceanic attributes provides clear targets for optimizing largehead hairtail conservation efforts in the East China Sea. We suggested that the eastern and southern areas of TCZ should be included in conservation planning for an effective management within a network of marine protected areas.