Background Climate extremes are likely to become more common in the future and are expected to change ecosystem processes and functions. As important consumers of seeds in forests, rodents are likely to affect forest regeneration following an extreme weather event. In April 2015, we began a field experiment after an extreme snowfall event in January 2015 in a primary forest that was > 300 years old. The heavy snow broke many tree limbs, which presumably reduced the numbers of seeds produced. Two treatments (rodent exclusion and rodent access) were established in the forest, in which rodent exclusion were achieved by placing stainlessness nets around the plot borders. Plant abundance, plant species richness, soil properties, soil microbial community composition, basal and substrate-induced respiration were determined in December 2017. Results Plant abundance and species richness significantly increased, but soil microbial biomass decreased with rodent exclusion. Urease activity and soil basal respiration also significantly decreased with rodent exclusion. Most other soil properties, however, were unaffected by rodent exclusion. The relative effects of multiple predictors of basal respiration were mainly explained by the composition of the soil microbial community. Conclusions After a heavy snowfall in an old-growth forest, exclusion of rodents increased plant regeneration and reduced microbial biomass and soil basal respiration. The main factor associated with the reduction in soil basal respiration was the change in the composition of the soil microbial community. These findings suggest that after a heavy snowfall, rodents may interfere with forest regeneration by directly reducing plant diversity and abundance but may enhance carbon retention by indirectly altering the soil microbial community.