The fishery resources and ecological environment in Shandong offshore are under great pressure. With the impact of exploitation activities such as coastal engineering and overfishing in Shandong, the fishery resources in this area are in decline, and the number of fish of high economic value is significantly reduced. To effectively monitor and manage the fishery resources, it is necessary to understand fishery ecosystem, for which biodiversity is a crucial index in community ecology research to indicate ecosystem status. To understand the spatial distribution of coastal biodiversity, and the relationships between biodiversity indices and environmental factors, this study used several diversity indices, including number of species, Simpson index, Shannon index, and Pielou index, to analyze the spatial distribution of biodiversity based on investigation data of fishery resources in 2017 winter in Shandong offshore. Owing to a lot of non-linear and non-additive processes in fishery ecosystem, random forest model is used to assess the relationship between diversity indices and environmental factors. The results showed that the spatial distribution of diversity indices varied substantially in the Shandong offshore area, with a trend of higher diversity in the southern area of the Peninsula than that in the north, which included Yanwei fishery ground, Laizhou Bay, and the southern Bohai Sea. The southern Bohai Sea had the lowest level of species diversity. Random forest model could be properly fitted to the diversity data, and the rate of explained deviation reaches 77.46% and 45.66% for species number and the Shannon diversity index, respectively. However, the regression model of Pielou index had a low proportion of explained deviation. The bottom temperature, salinity, and water Depth had significant influences on the diversity indices, significantly correlated with species number, diversity index, and evenness index. The effect of bottom sediment type was not significant on species number and two diversity indices, but was high for the Pielou evenness index. The results were also compared for fishery resource surveys at different scales. The conclusion is that surveys of similar scale are necessary for long-term monitoring of biodiversity. This study systematically analyzes the diversity pattern of Shandong offshore ecosystem and provides scientific support for long-term marine ecosystem monitoring and specific marine management. We highlight the necessity of protecting biodiversity in order to restore fishery resources. Decisions could be made based on the level of biodiversity in terms of habitat restoration and the establishment of protected areas.