The effects of low-intensity and high-frequency prescribed burning on the soil CO2 emissions from Pinus yunnanensis forestland should be explored to achieve sustainable operation and management under fire disturbance. A Li-6400XT portable photosynthesis meter (equipped with a Li-6400-09 soil respiration chamber) and a TRIME®-PICO 64/32 soil temperature and moisture meter were used to measure the soil CO2 flux, soil temperature, and soil moisture at fixed observation sites in two treatments (i.e., unburned (UB) and after prescribed burning (AB)) in a Pinus yunnanensis forest of Zhaobi Mountain, Xinping County, Yunnan, China from March 2019 to February 2021. We also determined the relationships between the soil CO2 flux and soil hydrothermal factors. The results showed that (1) the soil CO2 flux in both UB and AB plots exhibited a significant unimodal trend of seasonal variations. In 2020, the highest soil CO2 fluxes occurred in September; they were 7.08 μmol CO2·m−2·s−1 in the morning and 7.63 μmol CO2·m−2·s−1 in the afternoon in the AB treatment, which was significantly lower than those in the UB treatment (p < 0.05). The AB and the UB treatment showed no significant differences in annual soil carbon flux (p > 0.05). (2) The relationship between the soil CO2 flux and moisture in the AB and UB plots was best fitted by a quadratic function, with a degree of fitting between 0.435 and 0.753. The soil CO2 flux and soil moisture showed an inverted U-shaped correlation in the UB plot (p < 0.05) but a positive correlation in the AB plot (p < 0.05). Soil moisture was the key factor affecting the soil CO2 flux (p < 0.05), while soil temperature showed no significant effect on soil CO2 flux in this area (p > 0.05). Therefore, the application of low-intensity prescribed burning for fire hazard reduction in this region achieved the objective without causing a persistent and drastic increase in the soil CO2 emissions. The results could provide important theoretical support for scientific implementation of prescribed burning, as well as scientific evaluation of ecological and environmental effects after prescribed burning.