The Bohai Sea is a semi-enclosed marginal sea in the North West Pacific. Meiofauna samples were collected from 22 stations in the Bohai Sea to document the spatial distribution, structure, and diversity of the meiofaunal community and investigate the major factors influencing the community features. A total of 20 higher taxa of meiofauna were identified. The dominant group was Nematoda, accounting for 90.8% of the total meiofaunal abundance on average, followed by Copepoda, Bivalvia, Polychaeta, Kinorhyncha, and Ostracoda. Meiofaunal abundance ranged from 121 ± 89 ind (10 cm2)−1 to 3042 ± 1054 ind (10 cm2)−1. Diversity indices also varied among different stations, with a Margalef’s richness index (d) of 1.1–3.1, Shannon-Wiener diversity index (H′) of 0.7–1.8, and Pielou’s evenness index (J′) of 0.4–0.8. Meiofaunal abundance and diversity indices were significantly lower in the areas of Bohai Bay and adjacent to Laizhou Bay. The correlation analysis showed that meiofaunal abundance and diversity indices are closely linked to variations in sediment silt-clay content, medium grain size (MDΦ), and chlorophyll-a concentrations. The ecological quality status of most stations can be ranked from poor to moderate based on meiofaunal richness. According to the value of nematode to copepod ratio (Ne:Co ratio), most stations are uncontaminated, except seven stations are slightly or moderately contaminated. Both meiofaunal richness and Ne:Co ratio indicate the poor ecological quality of three stations adjacent to Laizhou Bay. The efficiency of the meiofauna communities as environmental indicators will be tested in a greater area in the future studies.