Precipitation and temperature in the subalpine region have increased dramatically in recent decades due to global warming, and human disturbances have continued to impact the vegetation in the region. Seed bank plays an important role in population recovery, but there are few studies on the synergistic effects of human disturbances and climate change on seed bank. We analyzed the synergistic effects of human disturbances and climate change on seed bank samples from 20 sites in the subalpine coniferous forest region using grazing and logging as the disturbance intensity gradient and precipitation and temperature as climate variables. The species diversity of aboveground vegetation all changed significantly (p < 0.05) with precipitation, temperature and disturbance level, while the seed bank richness and density did not. Furthermore, the species composition of the seed bank varied significantly less than that of the aboveground vegetation at different levels of disturbance (p < 0.001). Thus, seed bank showed a strong buffering capacity against the risk of local extinction caused by environmental changes that shift the species composition and diversity of aboveground vegetation. In addition, soil and litter are important influences controlling seed bank density in subalpine forests, and the results of structural equation modelling suggest that both disturbance and climate change can indirectly regulate the seed bank by changing the physicochemical properties of soil and litter. We conclude that increases in precipitation and temperature driven by climate change can buffer the negative effects of disturbances on the seed bank.