The ecological environment in southern Yunnan is fragile with serious land degradation. Economic orchard, as a major ecological management, has a certain effect on organic carbon sequestration. Reasonable planting patterns can improve resource utilization efficiency through the complementarity between species, increasing the quality of soil carbon pool and obtaining higher comprehensive benefits. This study was carried out on different planting patterns of peach single species (SP) and peach pumpkin interplanting (PP), located in Taoyuan Village, Kaiyuan City, Yunnan Province. Taking the adjacent natural forest (CK) as control, soil organic carbon (SOC), permanganate oxidizable carbon (POXC), particulate organic carbon (POC), and mineral-associated organic carbon (MAOC) were measured in 0-40 cm soil layer at an interval of 10 cm. Meanwhile, we calculated carbon pool activity index (CPAI), carbon pool index (CPI) and carbon pool management index (CPMI). Our objective was to investigate the effects of peach tree planting patterns on the stability of soil organic carbon and CPMI and clarify the relationship between soil organic carbon fractions and soil physicochemical properties. The results showed that the content of soil organic carbon fractions of the peach tree planting patterns and the control decreased with the increase of soil depths, the average SOC content were 14.68 g/kg (CK), 9.57 g/kg (PP), 8.58 g/kg (SP), respectively. The proportion of average POC, POXC and POC/MAOC showed as SP>CK>PP. PP had a lower proportion of active organic carbon with better organic carbon stability. Moreover, the CPMI of both peach tree planting patterns were lower than CK and reached the maximum value in the layer of 10-20 cm. SP had a higher CPAI (1.10), while PP had a higher CPMI (69.51), indicating that the stability and quality of PP soil carbon pool was better than that of SP. SOC, POXC, POC, and MAOC were all significantly positively correlated with sand, C/N, available phosphorus, exchangeable potassium, pH, and total phosphorus (in order of correlation). Peach tree planting patterns, soil depth and their interaction had different effects on soil organic carbon fractions and its proportion. Redundancy analysis also showed that sand and pH were the main environmental factors affecting the soil organic carbon fractions and soil organic carbon pool under different peach tree planting patterns and soil depths. We concluded that peach tree planting patterns changed the SOC and its fractions. Here, we consider PP as a better planting pattern, which is beneficial to organic carbon sequestration. Appropriate management measures should be taken according to the soil properties, basic situation of carbon pool and the effectiveness of nutrients such as nitrogen and phosphorus, so as to enhance the carbon sequestration efficiency and carbon sink level while improving the economic benefits.