Stem surface CO₂ effluxes are an important part of the carbon (C) budget of forest ecosystems, which play an important role in sustaining global C balance. In recent years, global changes have altered the supply of plant photosynthates, and this could affect plant stem surface CO₂ effluxes. However, the underlying mechanisms of how changes in plant photosynthates affect stem surface CO₂ effluxes are still unclear. In the present study, potted Chinese fir (Cunninghamia lanceolata) seedlings were used, and shading was applied to alter the supply of photosynthate. We measured stem surface CO₂ effluxes using a Li-8100 Automated Soil Gas Flux System, and measured the concentrations of stem soluble sugar, starch, non-structural C, and stem temperature to clarify the effects of shading on stem surface CO₂ effluxes. The results showed that the concentrations of stem soluble sugar, starch, and non-structural C were significantly reduced by 55.0%, 78.9% and 64.3%, respectively. The mean stem surface CO₂ effluxes significantly decreased by 39.9% during shading, and the decrease rate gradually increased as shading time increased. Moreover, shading decreased the temperature sensibility of stem surface CO₂ effluxes. The stem surface CO₂ effluxes and the concentrations of stem soluble sugar, starch, non-structural C, and stem temperature were recovered after regaining normal light conditions, as compared with the control. These results suggest that the changes in photosynthate supply could affect stem surface CO₂ effluxes and consequently global C cycling by regulating the response of stem surface CO₂ effluxes to temperature.