The elevation gradient may affect soil organic matter through a variety of environmental factors. The soil organic carbon pool is an important component of soil organic matter; its any slight changes may have an extremely important impact. Therefore, there may be variations in the soil carbon pool at different elevations. Soil organic carbon is an important indicator of soil fertility, which is affected by various factors, including soil physical and chemical properties and microorganisms. Pinus taiwanensis Hayata, which is an excellent tree species for afforestation and timber in high mountain areas, has recently experienced a decline in the high altitudes of Daiyun Mountain Nature Reserve. A study of the change in soil organic carbon fractions along the elevation gradient in the P. taiwanensis forests of Daiyun Mountain Nature Reserve can therefore not only provide a scientific basis for estimation of the carbon pool in this region, but also can help to elucidate the mechanisms influencing the growth and change in the dynamics of the P. taiwanensis forest. Therefore, in this study, the P. taiwanensis forests of Daiyun Mountain along different elevation at 1300 m (L), 1450 m (M), and 1600 m (H) were analyzed for the basic physicochemical properties, organic carbon fractions, and microbial characteristics of the soil. Our results showed that the soil nutrient content first increased and then decreased along the elevation gradient, and was consistent with the trends in the soil carbon fractions. The microbial biomass carbon and microbial biomass nitrogen were both the highest at M altitude (1450 m), and the elevation gradient had no significant effect on carbon hydrolase. A redundancy analysis showed that total nitrogen was the most important factor that affected the change in soil organic carbon, followed by the carbon/nitrogen ratio. Therefore, in the case of a small elevation span, it was mainly nitrogen, rather than temperature, that affected the change in soil organic carbon. The high-altitude area with a high recalcitrant carbon pool ratio may aggravate the growth dilemma of the P. taiwanensis forests in this area in the future, thereby affecting the carbon pool in this region.