Abstract: Microorganisms in deep-sea surface sedimentary environments are key components of global biogeochemical cycles and play important roles in marine ecosystems, while studies on their diversity and spatial distribution are still limited. In this study, prokaryotic microbial diversity on surface sediments from the Tropical Southeast Pacific Ocean was analyzed based on 16S rRNA gene high-throughput sequencing. The results showed that the dominant groups of prokaryotic microorganisms mainly included Thaumarchaeota (37.16%), Alphaproteobacteria (13.40%), Gammaproteobacteria (13.50%) and Chloroflexi (11.41%), etc., which are important members involved in aerobic processes such as ammonia oxidation and sulfur oxidation. For examples, ammonia oxidation in Thaumarchaeota may mediate the manganese oxidation. Other taxa, such as Magnetospiraceae may be involved in the iron reduction. Redundancy analysis (RDA) showed that the mass fractions of ∑REY (total rare earths), TFe₂O₃ (total iron oxides), MnO (manganese oxides) and Co (cobalt elements) significantly affected the community structure of the prokaryotic microorganisms in the surface sediments, especially Thaumarchaeota (OTU level). The group with high quality scores in four environmental factors showed a strong correlation between microbial composition and environmental variables. The phylogenetic results showed that Thaumarch- aeota formed different phylogenetic branches, which were closely related to the substrate property and chemical elements content. This study provides basic information for understanding the function of deep-sea ecosystems and the process of seafloor mineralization.