Drought poses a severe threat to grassland biodiversity and ecosystem function. However, quantitative frameworks that capture the interactive effects of drought intensity and duration on productivity remain scarce, limiting impact assessment accuracy. To bridge this gap, we developed and validated a novel hybrid modeling framework to quantify drought impacts on net primary productivity (NPP) across Inner Mongolia’s major grasslands (1961–2012). Drought was characterized using the Standardized Precipitation Index (SPI), and ecosystem productivity was simulated with the Biome-BGC model. Our core innovation is the hybrid model, which integrates linear and nonlinear components to explicitly capture the compounded, nonlinear influence of combined drought intensity and duration. This represents a significant advance over conventional single-perspective approaches. Key results demonstrate that the hybrid model substantially outperforms linear and nonlinear models alone, yielding highly significant regression equations for all grassland types (meadow, typical, desert; all p < 0.001). Independent validation confirmed its robustness and high predictive skill (NSE ≈ 0.868, RMSE = 20.09 gC/m²/yr). The analysis reveals two critical findings: (1) drought duration is a stronger driver of productivity decline than instantaneous intensity, and (2) desert grasslands are the most vulnerable, followed by typical and meadow grasslands. The hybrid model serves as a practical tool for estimating site-specific productivity loss, directly informing grassland management priorities, adaptive grazing strategies, and early-warning system design. Beyond immediate applications, this framework provides a transferable methodology for assessing drought-induced vulnerability in biodiverse ecosystems, supporting conservation and climate-adaptive management.