Based on the data of the fisheries resources survey in the Zhoushan Changbai sea area in October 2016 (autumn) and April 2017 (spring), the ecological niche, interspecific ecological relationship, and ecological niche differentiation of the major nekton species were studied using the methods of niche breadth, niche overlap, and redundancy analysis (RDA). The results showed the presence of 11 and 8 major nekton species in spring and autumn, respectively, with large differences between the niche breadth values obtained in the two seasons. It is observed that there are three kinds of both wild ecological species and middle niche species in spring, and two in autumn, with five and four narrow niche species in spring and autumn, respectively. A significant positive correlation existed between the index of relative importance (IRI) and niche breadth value (Bi). The degree of niche overlap of the major nekton species was unbalanced, being relatively high in autumn, with the species pairs of O_ik > 0.6 accounting for 42.86% of the total niche overlap. The degree of niche overlap of the major nekton species was relatively low in spring, accounting for only 21.82% of the total niche overlap. The RDA showed that temperature and salinity were the factors directly affecting the distribution of the major nekton species, while dissolved oxygen, suspended matter, and pH were also important factors. The major nekton species showed ecological differentiation in these resource dimensions. In summary, the major nekton species that were distributed in the waters of Daiquyang and the area adjacent to the mouth of Hangzhou Bay showed an overall low trophic level, but had a large niche breadth. Some of the traditional high-trophic level and typical economic species were replaced with the general or rare species of narrow niche breadth, for example, Larimichthys crocea and Nibea albiflora, etc. A significant reduction was observed in their community species, resources, stability along with the degradation of community structure and function. Therefore, it is of great significance and urgent to strengthen the monitoring, protection, and management of nekton in the Zhoushan Changbai sea area.