Seamounts are recognized as biological hotspots in the ocean, hosting diverse microorganisms, and exert complex influences on the organisms living in surrounding seawaters. However, the influence of seamount elevation on niche partition of sediment microbes remains poorly understood since limited samplings. Here we collected surface sediments from three slopes covering full elevations of two seamounts. Elevation determined the significant divergence of microbial community structures along vertical gradients, and frequent interactions was a potential strategy in the adaption of environmental stress. Random forest and adjusted T-test consistently showed that the genes associated to motility, biofilm formation, complex polysaccharides utilization, and stress adaption in lower slope were more abundant than those in upper slope, indicated that microorganisms from lower slopes exhibit superior environmental stress tolerance. Instead, upper-slope microorganisms were highly enriching in genes related to simple carbon utilization and nitrogen cycle. Collectively, these findings clarify the role of seamount elevation in shaping sediment microbes, offering insights to inform seamount ecosystem protection and management.