Based on the data of China Geochemical Baselines project, geostatistical analysis was used to investigate the spatial variations in soil organic carbon (SOC), total nitrogen (TN) and total phosphorus (TP) contents across the "Three Rivers" regions of southwest China, and the factors affecting them were analyzed by the redundancy analysis (RDA) and Person's correlation. Results showed that, the average content of SOC, TN and TP in the study area were 7.20 g/kg, 0.84 g/kg and 0.55 g/kg, respectively. The SOC and TN contents showed an obvious enrichment characteristic with great spatial variability, while TP content was stable on regional scale. The SOC, TN and TP contents decreased with elevation increase in the northern frigid highland, but showed an opposite character in the southern tropical & subtropical, which actually reflected the control of temperature on them. Combined with that there were higher SOC, TN and TP contents in subalpine meadow soil and red earth-yellow earth of the middle latitude zone, these suggested that the suitable temperature was conducive to the accumulation of soil nutrients. The weak positive correlation between population density and soil nutrients, together with high level of soil nutrients in the vicinity of large cities, demonstrated that human activities had significantly increased the soil nutrients contents in the study area. The RDA results showed that soil nutrients in the northern frigid highland were mainly controlled by the environmental factors dominated by temperature and soil structural factors dominated by parent materials with the total explanatory power as high as 75.87%, while in the southern tropical & subtropical mainly by the environmental factors dominated by chemical and biological weathering and the biological factors dominated by vegetation with the total explanatory power as high as 88.53%. The above factors superimposing a certain degree of human activities converged to cause that the SOC and TP contents in the south were higher than that in the north while the TN content was lower than that in the north.