In order to explore the distribution of soil carbon, nitrogen and phosphorus storage in Karst forest in the Lijiang River Basin, and to provide a theoretical basis for protecting the fragile Karst ecosystem in the Lijiang River Basin, a total of 15 natural forest quadrats of 20 m × 20 m were set up in the typical Karst forests in the upper, middle and lower reaches of the Lijiang River, and the forest vegetation was surveyed for each tree. The 0-20, 20-40 cm soil layers were collected by five-point collection method to analyze the spatial distribution of soil carbon, nitrogen and phosphorus storage and driving factors, and to quantify the contribution of various biological and abiotic factors to the formation of soil nutrient storage pattern in karst forest. The results showed that: (1) The average distribution of soil carbon, nitrogen and phosphorus storage in the Karst forest in the Lijiang River Basin was upstream > downstream > midstream. In the Karst forest soil of the Lijiang River Basin, the storage of carbon, nitrogen and phosphorus was 55.8~192.0, 3.1~14.8, and 6.0~12.0 kg/m², respectively. The storage of carbon and nitrogen in 20 cm soil layer in the same watershed was significantly higher than that in 20-40 cm soil layer, while phosphorus storage did not show significant difference in the soil layers of different depth in the Lijiang River Basin. (2) Carbon storage showed a significant positive correlation with C/P, N/P, Shannon-Wiener index and Simpson index of forest species diversity; nitrogen storage had a significant positive correlation with C/P, N/P, Shannon Wiener index and Simpson index, while a significant negative correlation with C/N; the phosphorus storage had a significant negative correlation with C/N, and there was no significant correlation with forest species diversity. (3) The stoichiometric characteristics of Karst forest soil chemistry in the Lijiang River Basin were the direct driving factors driving the distribution of soil carbon, nitrogen and phosphorus storages, and the stoichiometric characteristics of deep soil were the most important direct driving factors. Secondly, forest species diversity played an important role in the immobilization and input of soil nutrients, directly affecting and driving the formation of soil carbon and nitrogen storage distribution pattern. The formation of phosphorus storage was not driven by the impact of forest vegetation conditions. In the Karst forest soil in the Lijiang River basin, the stoichiometric characteristics and the diversity of forest plants had played an important role in the formation and decomposition of soil carbon, nitrogen and phosphorus reserves. It is advocated to improve the water and fertilizer storage functions of forest soil in the Lijiang River Basin by improving the species diversity of forest vegetation in the Lijiang River Basin, while protecting the fragile karst forest ecosystem in the Lijiang River Basin.