The fish community structure and its relationships with the environmental factors in the Nature Reserve of Trichiurus japonicus were studied based on the data collected from bottom trawl surveys in spring and autumn 2014 by using non-metric multi-dimensional scaling (NMDS), canonical correspondence analysis (CCA) and classification and regression tree (CART). In spring, a total of 75 fish species were sampled in the survey, belonging to 63 genera, 49 families, and 14 orders. In autumn, a total of 78 fish species were captured, belonging to 64 genera, 50 families, and 15 orders. Spatial structure of fish assemblage in spring and autumn could be classified into two groups. ANOSIM (analysis of similarity) indicated that the fish species composition varied significantly between two groups in two seasons. The canonical correspondence analysis (CCA) suggested that the main environmental factors affecting the spatial distribution of fish assemblage in spring and autumn were water temperature, salinity, depth and zooplankton. The average values of diversity index and richness index were 1.65±0.60 and 2.46±0.90 separately in spring, while the average values of diversity index and richness index were 1.42±0.53 and 1.89±0.60 separately in autumn. The classification and regression tree (CART) indicated that the diversity and richness index in spring and autumn were mainly affected by Chl.a, DO, depth, pH and zooplankton (euphausiid and planktonic larvae). The main factors affecting the diversity index were water temperature, depth and salinity in autumn, while the main factors affecting the richness index were water temperature and depth.