In order to reveal the spatio-temporal distribution of meiofaunal assemblages and its relationship with environmental factors in semi-enclosed bay habitats, meiofaunal and sediment samples were collected in February (winter), May (spring), August (summer) and November (autumn) 2014 in Jiaozhou Bay, China. A total of 20 meiofaunal taxa were identified. The most dominant group was free-living marine nematode, followed by benthic copepod. During the four sampling seasons, the values of meiofaunal average abundance were (912.3 ± 603.1), (1576.4 ± 659.5), (1074.6 ± 417.6), (2152.4 ± 1062.3) ind./10 cm2 while those of biomass were (575.0 ± 398.5), (874.3 ± 518.4), (617.9 ± 337.8), (1203.6 ± 719.6) μg dwt/10 cm2, respectively. In terms of vertical distribution, meiofauna were mainly found in the (0–2) cm sediment layer (59.92%), followed by (2–5) cm layer (28.25%) and (5–8) cm layer (11.82%). Results of correlation analysis showed that bottom water temperature was the main factor influencing meiofaunal distribution and food source (sediment organic matter content) was the main factor influencing meiofaunal assemblages.