Microeukaryotic diversity, community structure and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rDNA, we explored microeukaryotic communities from the “Haima” cold seep in the northern South China Sea. We compared three distinct habitats: active, less active and non-seep regions, with vertical layers (0–25 cm) from sediment cores. The results showed that seep region harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification at cold seep sediments. Microeukaryotic α-diversity at cold seep was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism at cold seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.