Natural forest-protection programs have been implemented to increase stand volume and forest ecosystem diversity, and to improve forest resources. However, they have had some negative influences on forests, such as high stand density and poor growth, and these can easily lead to insect outbreaks and fire disasters. Forest thinning can effectively eliminate the negative influences caused by natural forest protection management. Forest thinning programs have been conducted for several years and these approaches have led to reduced tree mortality and accelerated natural regeneration. However, it has been demonstrated that forest micro-climates influence soil CO₂ emissions. This study investigated the effects of forest thinning on soil CO₂ emissions using the Yasso07 model to simulate a pine-oak mixed forest in the Huoditang forest zone area of the Qinling Mountains. The topography of the Qinling Mountains is complicated and fractured, so it is difficult to duplicate experimental plots in a randomized block design. Therefore, the quadratic general rotary design was applied, and thinning and residue-removed intensity were the factors in the experiment. Thirteen experimental plots were selected, including five control levels and nine treatment plots. Five litter-fall collection frames (1 m × 1 m) were laid in each experimental plot. The litter fall was collected each month from September 2012 to September 2014. The ethanol-soluble, water-soluble, acid-soluble, and non-soluble compound contents in the leaf litter fall were determined. Although the technology to measure soil CO₂ emissions has continually improved, the soil spatial heterogeneity and strong soil carbon stability in undisturbed habitats has led to inaccuracies in the evaluation methods used in forest soil carbon dynamics research. Yasso07 is a soil-carbon decomposition model and is based on the assumption that there are four types of litter transformation. Yasso07 has been widely used in Europe and the United States because it can be operated easily; requires few parameters, which are easy to obtain; and the simulated results are reliable. However, there was no basis to determine if it could be applied in the Qinling Mountains. Therefore, this study validated the reliability of the Yasso07 model in this region. The soil CO₂ emission traits under different thinning and residue-removed intensities were analyzed based on simulations by the model. The following results were obtained: (1) there was a significant difference between the conifer and broadleaf litter chemical compositions. The ethanol and water soluble compound contents were significantly higher in the conifer tree litter than in the broadleaf tree litter, and the non-soluble compound content was significantly lower in conifer litter than in broadleaf litter. (2) The chemical composition of the litter fall significantly affected soil CO₂ emissions, and (3) thinning intensity was the key factor affecting CO₂ emissions. Soil CO₂ emissions increased after forest thinning, and when the thinning and residue-removed intensities were 12.38% and 53.18%, respectively, the soil CO₂ emission fell to a minimum of -15.318 Mg hm^-2 a^-1.