The unique geological characteristics of oceanic trenches affected the structure and ecological functioning of microbial communities, whereas little information is available on their population dynamics and assembly mechanisms. Here, diversity, composition and driving forces for the free-living (FL) and particle-associated (PA) bacterial communities in the benthic boundary layer (BBL) of five different trenches, the Kermadec, Diamantina, Wallaby-Zenith, Yap and Mariana trenches, were explored using high-throughput sequencing. The clustering of microbial communities was based on geographical heterogeneity rather than size-fractions, and those located in the northern (Cluster II) and southern (Cluster I) hemispheres formed two distinct clusters, and mainly affected by NO₃^- + NO₂^-. Comparatively, significantly lower levels of biodiversity and higher gene abundance were detected in the Cluster I, along with a low community complexity revealed by network analysis. These discrepancies might be explained by the geographic separation and tectonic activity. Clear distance-decay distribution of microbial communities was disclosed and mainly driven by dispersal limitation of stochastic process. More positive interactions detected signified that most bacteria were cooperative in trench ecosystem. More shared genera than specific ones were found between PA and FL. Higher ratio of PA/FL gene abundance in the BBL might due to more resuspended particles derived from the benthic sediment. These findings provided new perspective on the assembly mechanism of microbial communities across multiple trenches, and will improve our understanding of geographical patterns and ecological functions of the unique deep-sea ecosystems.