Many previous studies have focused on leaf litter decomposition in tropical ecosystems, but our understanding of the effect of root diversity on decomposition and soil respiration is still unclear. We investigated the decomposition of fine-roots from 21 dominant tree species from a tropic forest in a long-term, well-replicated incubation experiment with varying levels of root diversity. We measured fine-root mass loss and soil CO2 release and analyzed potential microbial drivers and related soil properties. Our results showed that as fine-root litter diversity increased, soil properties, microbial diversity, and fungal biomass changed nonlinearly, leading to the highest mass loss and soil CO2 release in the moderate diversity treatment group. Indirect effects of soil properties and microbial communities were larger than the direct effect of fine-root diversity. Our findings suggest that root diversity has a nonlinear effect on soil respiration during decomposition and emphasize the importance of protecting biodiversity.