Biological invasion is one of the most important factors affecting global biodiversity change, which can adversely affect ecosystem function. However, little is known about the effects of belowground biological invasions on soil ecosystems. In this study, we conducted a field-based mesocosm experiment to observe the effects of exotic and native earthworms (Pontoscolex corethrurus and Amynthas corticis, respectively) on soil nutrients and micro-decomposers (i.e., soil microorganisms and nematodes) in a subtropical forest in southern China. We found that exotic and native earthworms had different effects on nutrient availability and nematode communities in the soil. Specifically, exotic earthworms significantly decreased the content of nitrates in the soil and tended to decrease the total nematode abundance compared with native earthworms. Furthermore, nematode species richness and Shannon–Wiener index were lowest in the treatment with exotic earthworms and were the highest in the treatment with native earthworms. However, neither native nor exotic earthworms significantly affected soil microbial community composition. The results of redundancy analysis indicated that available phosphorus was positively correlated with nematode community. Our results demonstrated that exotic earthworms had adverse effects on the available nutrient content in the soil, and had a potential negative effect on the abundance of soil microfauna. These findings will be helpful in understanding the influence of exotic earthworms on soil micro-decomposers and the ecological consequences of earthworm invasion.