The coastal waters of Shandong have rich fisheries resources but have suffered from pressures including overfishing. In order to comprehensively understand the composition and structure of the fish community in Shandong coastal waters and to provide a scientific basis for the conservation of fishery resources, a fishery resources survey was conducted in Shandong coastal waters from 2016 to 2017 using bottom trawl in four seasons. A range of multivariate statistical methods including non-metric multi-dimensional scaling (NMDS) and ANOSIM were used to analyze the species composition and spatial heterogeneity of the community structure. The results showed that a total of 134 species were caught in this survey, of which 53 species had Index of relative importance IRI ≥ 1. NMDS analysis showed that the 53 species could be divided into three groups, a, b, c. Among them, Group a was characterized by the large biomass in summer and Group c in autumn. Group b was characterized by the relatively small changes of biomass throughout the year and the obvious dominance in spring and winter. Regarding the spatial structure of fish community, NMDS and ANOSIM showed that the fish community structure in Laizhou Bay (Zone A) was significantly different from that in the northern and southern adjacent waters (Zones B and C) of the Shandong Peninsula, and the differences persisted in all seasons. SIMPER showed that the species that caused the spatial heterogeneity of community structure between Zone A and Zone B & C were Cynoglossus joyneri and Lophius litulon in spring; Engraulis japonicus in summer; Chelidonichthys kumu in autumn; Acanthogobius ommaturus and L. litulon in winter.