Due to their extreme water depths and unique physicochemical conditions, deep-sea ecosystems develop uncommon microbial communities, which play a vital role in biogeochemical cycling. However, the differences in the compositions and functions of the microbial communities among these different geographic structures, such as seamounts (SM), marine trenches (MT), and cold seeps (CS), are still not fully understood. In the present study, sediments were collected from SM, MT, and CS in the Southwest Pacific Ocean, and the compositions and functions of the microbial communities were investigated by using amplicon sequencing combined with in-depth metagenomics. The results revealed that significantly higher richness levels and diversities of the microbial communities were found in SM sediments, followed by CS, and the lowest richness levels and diversities were found in MT sediments. Acinetobacter was dominant in the CS sediments and was replaced by Halomonas and Pseudomonas in the SM and MT sediments. We demonstrated that the microbes in deep-sea sediments were diverse and were functionally different (e.g., carbon, nitrogen, and sulfur cycling) from each other in the seamount, trench, and cold seep ecosystems. These results improved our understanding of the compositions, diversities and functions of microbial communities in the deep-sea environment.