Climate warming can be detrimental to biodiversity and ecosystem multifunctionality. Numerous studies have examined the effect of warming on ecosystem multifunctionality; however, little is known about how long-term warming affects ecosystem multifunctionality and its seasonal dynamics. Here, we determined the effects of long-term (10 years) in-situ soil warming on multitrophic diversity (plants, soil bacteria, soil fungi, arthropods, and nematodes) and soil multifunctionality in an alpine meadow. The effects of warming on multitrophic diversity were inconsistent, showing a positive effect on soil microbial diversity, including bacterial diversity and fungal diversity, in the upper layer (0–10 cm), a negative effect on plant diversity, and no effect on soil fauna diversity in either the upper (0–10 cm) or lower soil layers (10–20 cm). Warming had a minor effect on soil multifunctionality, and reduced seasonal differences in soil multifunctionality in upper soil layers, but expanded the differences in the lower soil layers. Based on structural equation models, both abiotic factors (soil water content and soil pH) and biotic factors (microbial diversity and fauna diversity) jointly influenced soil multifunctionality, with abiotic factors having a greater effect than biotic factors. The findings provide insights in the important effects of long-term warming on seasonal dynamics of soil multifunctionality, and the crucial role of multitrophic diversity for maintaining the sustainable development of the alpine ecosystem under climate warming.