By attaching to sinking particles, marine microbes can disperse vertically through the water column and reach the deep ocean. However, how in situ particle dynamics regulate microbial dispersal with increasing water depth the consequences of this process for deep-sea carbon cycling remain poorly understood. To assess microbial vertical connectivity, functional potential, and implications for deep-sea carbon cycling, we analyzed metagenomic data from two biogeochemically distinct regions of the South China Sea (SCS)—the continental slope and the oligotrophic central basin—and reconstructed metagenomic-derived functional gene catalogs and metagenome-assembled genomes (MAGs). Our results show that regional particle dynamics regulate vertical microbial dispersal and community assembly in the deep ocean, with important consequences for carbon transformation processes. Particle-associated microorganisms at water depths ≥ 2,800 m exhibit enriched genes involved in the degradation of recalcitrant organic matter and active foraging traits. In the oligotrophic central basin, longer particle sinking trajectories and stronger environmental selection promote persistent particle attachment and enhance vertical microbial dispersal. In contrast, rapid particle turnover on the continental slope limits transport on sinking particles and weakens the coupling between particle flux and microbial connectivity. Vertically transported surficial (“seed”) MAGs that appear enriched at bathyal depths harbor high abundances of genes associated with environmental sensing, signal transduction, oxidative stress responses, DNA and mismatch repair, and utilization of diverse carbon substrates, collectively suggesting genomic traits that support persistence during vertical transport and contribute to carbon transformation through the biological pump. Our findings demonstrate that regional particle dynamics govern microbial vertical connectivity and dispersal, thereby shaping the functional potential of deep-sea microbial communities and influencing carbon cycling in bathypelagic waters.