To study the effect of thinning intensity on the carbon sequestration by natural mixed coniferous and broadleaf forests in Xiaoxing’an Mountains, China, we established six 100 m × 100 m experimental plots in Dongfanghong Forest that varied in thinning intensity: plot A (10%), B (15%), C (20%), D (25%), E (30%), F (35%), and the control sample area (0%). A principal component analysis was performed using 50 different variables, including species diversity, soil fertility, litter characteristics, canopy structure parameters, and seedling regeneration parameters. The effects of thinning intensity on carbon sequestration were strongest in plot E (0.75), followed by D (0.63), F (0.50), C (0.48), B (0.22), A (0.11), and the control (0.06). The composite score of plot E was the highest, indicating that the carbon sequestration effect was strongest at a thinning intensity of 30%. These findings provide useful insights that could aid the management of natural mixed coniferous and broadleaf forests in Xiaoxing’an Mountains, China. This information has implications for future studies of these forests, and the methods used could aid future ecological assessments of the natural forests in Xiaoxing’an Mountains, China.