The supersaturation of methane is consistently observed in oligotrophic oxygen-enriched surface seawater, however, mechanisms responsible for this methane paradox are not fully understood. Atmospheric deposition is one of the most important sources of nutrients in the open ocean, which could potentially affect the nutrient structure and microbial activity in the upper ocean. In this study, we investigated the pathways of methane production and provided evidence for the regulation of atmospheric deposition on methane production in the Northwest Pacific Ocean. We found that methane was predominantly produced from C-P cleavage through methylphosphonate (MPn) decomposition. Atmospheric nitrogen deposition enhanced methane production from MPn by elevating heterotrophic activity and accelerating the environmental phosphorus limitation. Furthermore, aerosol deposition led to a shift of microbial communities dominated by phosphonates-utilizing prokaryotes (i.e., Rhizobiales, Rhodobacterales and Oceanospirillales), thereby facilitating methane production from C-P cleavage. Rhizobiales are a better competitor for phosphonates than other bacteria, suggesting the important role of N₂ fixers to drive DOP cycling in P-stressed environments. These results revealed an important linkage between atmospheric deposition and microbial methane production and provided novel insights into methane cycling in the oligotrophic open ocean.