As an important means of near-natural management in secondary forests, thinning effectively enhances the growth status of forest trees, and increases the overall forest yield and carbon sequestration capacity of the forest floor through rational stand regulation. This study focused on subtropical secondary broadleaf forests in the mountainous regions of western Zhejiang, China, and involved three treatment groups: a high-intensity thinning group (HT) (retaining trees with a diameter greater than 8 cm and removing shrub-layer vegetation), a low-intensity thinning group (LT) (retaining trees with a diameter greater than 5 cm and removing shrub-layer vegetation), and a control plot (no thinning treatment) (CK). The study aimed to investigate the effects of different thinning intensities on forest carbon stocks, soil respiration, and soil environmental factors, as well as to assess how thinning modifications impact the carbon sequestration capacity of the forest floor. The results illustrate the following: (1) The biomass growth and carbon sequestration capacity of individual trees under HT were significantly greater compared to other treatment groups. Conversely, carbon stock growth in the arboreal layer was higher under LT than under other treatments. (2) Thinning operations increased soil carbon stocks and improved soil fertility. (3) High-intensity (HT) and low-intensity thinning (LT) increased the soil moisture in both the surface and subsurface layers, with HT showing the highest levels. (4) One year after thinning, the soil organic matter (SOM) increased significantly, rising by 30.86% in HT and 21.84% in LT compared to CK. (5) In comparison to LT and CK, HT showed a significant increase in soil respiration rates, which led to higher CO2 and N2O emissions from the soil while also suppressing CH4 uptake. The study concludes that LT can enhance carbon sequestration in both the tree and soil layers, improve soil fertility, and reduce greenhouse gas emissions. This supports the sustainable development of forest ecosystems and effective carbon management.