Microorganism-mediated nitrogen (N) denitrification and dynamics are crucial ecosystems functions that influence N losses. However, the drivers and microbial mechanisms underlying seasonal variations in denitrification across elevations in alpine forest mountain ecosystems remain poorly understood. Here, we assessed the variations in potential denitrification rates and denitrifier communities using ¹⁵N-labeling techniques and high-throughput sequencing, and examined soil properties across an elevational gradient in alpine forest mountains. Our findings demonstrated that soil potential denitrification rates decreased with increasing elevations, exhibiting lower levels during the wet season (0.095 ± 0.005 mg kg^-1 d^-1) compared to the dry season (0.12 ± 0.007 mg kg^-1 d^-1) (P < 0.05). Soil substrates, including NH₄⁺-N, dissolved organic nitrogen, and total nitrogen, were identified as pivotal regulators of soil denitrification during the dry season, indicating substrate-driven control. Conversely, microbial attributes (nirS and nosZ genes abundance), were the primary factors governing soil denitrification during the wet season, reflecting microbial regulation. Additionally, Bradyrhizobium emerged as the dominant genus contributing to denitrification rates in our study. Overall, our study underscored the diverse factors driving the seasonal dynamics of soil denitrification and provided critical insights to improve ecosystem models to better predict N losses under increasingly pronounced wet-dry precipitation patterns.