Climate warming has profound effects on terrestrial ecosystems, with biodiversity playing a crucial role in modulating ecosystem productivity responses. While extensive studies have investigated how plant species richness (α-diversity) influences aboveground productivity under warming conditions, the contributions of plant and soil microbial β-diversity to belowground net primary productivity (BNPP) remain poorly understood. In this study, we conducted a 6-year warming experiment in an alpine meadow to investigate the response patterns and drivers of BNPP, as well as the α- and β-diversity of plant and soil microbial communities. Our results showed that warming increased BNPP by 41.41%–90.3%, with biodiversity metrics collectively accounting for about 86% of the variation in BNPP. Notably, while climate warming significantly reduced the α-diversity of both plant (p = 0.067) and soil bacterial communities (p < 0.05), soil bacterial β-diversity showed a marked increase. The enhancement in soil bacterial β-diversity was closely linked to increased gene abundance associated with ammonification and nitrification processes, identified as key drivers of BNPP under warming conditions. These findings underscore the pivotal role of soil microbial β-diversity in supporting BNPP under warming conditions. Our study highlights the need to preserve belowground microbial heterogeneity to maintain ecosystem functioning and enhance carbon sequestration efforts in the face of global climate change.