To explore the community characteristics of meiofauna in different microhabitats in mangrove ecosystem and to supplement the research data of meiofauna in the understory of mangrove wetland in China, an investigation was conducted on meiofauna in Futian Mangrove Nature Reserve, Shenzhen in January 2021 to study the spatial distribution of meiofauna in sediment and on leaf litter, the influencing environmental factors were analyzed. 9 and 12 meiofauna taxa were identified from sediment and leaf litter, respectively. The abundance and biomass of meiofauna in sediment were significantly different among sections and among tidal levels, but the abundance and biomass of meiofauna on leaf litter showed weak spatial heterogeneity. Correlation analysis showed that the abundance and biomass of meiofauna in sediment and on leaf litter were not significantly correlated with the measured environmental factors. There was no significant difference of meiofauna community composition among sections and among tidal levels, but the difference was significant between sediment community and leaf litter community, which indicated that the community structure of mangrove meiofauna was affected by different microhabitats.