Bryophytes play an important role in biogeochemical cycles and functions in forest ecosystems. Global climate changes have led to the population decline of bryophytes; however, the effects of bryophyte loss on the soil organic carbon stock and microbial dynamic remain poorly understood. Here, bryophytes were artificially removed to simulate the loss of bryophytes in two forests in Southwest China, i.e., evergreen broad-leaved forest and temperate coniferous forest. Soil physicochemical properties, microorganisms, and soil organic carbon stocks were analyzed and factors regulating soil organic carbon stocks were explored. Results showed that bryophyte removal significantly decreased soil organic carbon in the coniferous forest but had a negligible effect on the evergreen broad-leaved forest. Bryophyte removal had an insignificant effect on soil properties and microbial PLFAs except that soil nitrogen significantly increased in the 0–10 cm layer in the evergreen broad-leaved forest, while soil temperature and bulk density increased in the coniferous forest in the 0–10 and 10–20 soil layers, respectively. Soil organic carbon stocks increased by 14.06% in the evergreen forest and decreased by 14.39% in the coniferous forest. In the evergreen forest, most soil properties and microorganisms contributed to the change of soil organic carbon stocks, however, only soil organic carbon and depth had significant effects in the coniferous forest. Our findings suggest that soil physiochemical properties and microorganisms regulated the different responses of soil organic carbon stocks after bryophyte removal in the two forests. More research is needed to better understand the effects of understory plants on soil organic carbon stocks in various forest ecosystems.