Mountain forests in biodiversity hotspots show complex responses to climate and topographic gradients. However, the effect of synergistic controls of elevation and climate on Net Primary Productivity (NPP) dynamics remain insufficiently quantified in complex mountains. Southwest China’s mountains are Asia’s most biodiverse temperate region with pronounced vertical ecosystem stratification, representing a critical continental carbon sink. This study investigated the spatiotemporal dynamics and driving mechanisms of NPP in Southwest China’s typical mountain ecosystems over the past three decades using a high-resolution modeling framework integrated with relative importance analysis, a Geodetector, and an elevation-dependent model. The results showed that (1) NPP revealed a significant increasing trend, rising from 634 ± 325 to 748 ± 348 g C m⁻² yr⁻¹ (mean rate 4 g C m⁻² yr⁻¹) from 1990 to 2018. Spatially, the most rapid increases occurred in eastern regions. (2) Rising CO₂ and climate warming (dominate 17% regions) drove interannual NPP growth, with elevation thresholds dictating driver dominance. The CO₂ governed low elevation, while temperature controlled higher elevation (>4800 m). (3) The elevation-dependent model revealed a more complex and nonlinear relationship between NPP and elevation, identifying three distinct phases: the saturation phase (3500 m) with continuously attenuated NPP losses (NPP average loss of 10.5 g C m⁻² yr⁻¹ per 100 m) reflecting high-elevation vegetation adaptation to extreme conditions. (4) Land cover dominated NPP spatial heterogeneity and was amplified by interactions with elevation and temperature, highlighting a vegetation–climate–topography coupling mechanism that critically shapes productivity patterns. Biodiversity-rich widespread mixed forests underpinned the region’s high productivity. Mountain protection should focus on protecting existing evergreen forests from fragmentation, while forestation should prioritize the establishment of biodiversity-rich mixed forest. These findings established a comprehensive framework for spatiotemporal analysis of driving mechanisms and enhanced the understanding of NPP dynamics in complex mountain ecosystems, informing sustainable management priorities in mountain regions.