Researchers are paying increasing attention to soil stoichiometry (carbon:nitrogen:phosphorus (C:N:P) ratios) in efforts to explore biogeochemical cycles, but little is known about the spatial pattern, implications, and driving factors of this stoichiometry in large, ecologically fragile areas. To explore these factors, we established three transects that covered a total length of about 4300 km in ecologically fragile areas of China, and sampled at intervals of about 25 km. These transects covered the karst area and the agro-pastoral ecotone of southwestern China, the Qinghai-Tibet Plateau, the Loess Plateau, and the forest-grassland ecotone. We collected 312 soil samples to a depth of 30 cm from 156 plots. The soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) in the ecologically fragile areas showed strong coupling relationships. Soil C:N:P was 51:4:1 to a depth of 30 cm, which is lower than the average global C:N:P (111:8:1). SOC and TN concentrations at 0 to 20 cm were significantly higher than that at 20 to 30 cm, but TP did not differ significantly among depths. SOC, TN, and TP concentrations were highest in the agro-pastoral ecotone, and were lowest in the Loess Plateau. C:N, C:P, and N:P were highest in the karst area. C:N were lowest in the Qinghai-Tibet Plateau, and C:P and N:P were lowest in the Loess Plateau. The spatial pattern of C, N, and P stoichiometry along environmental gradients was variable. The contributions to explaining the soil stoichiometry were highest for climate (21.7%), vegetation (8.9%), soil properties (6.4%), and topography (0.6%) to a depth of 20 cm, versus vegetation (35.9%), climate (5.3%), soil properties (3.3%), and topography (2.1%) at 20 to 30 cm. The results provide new insights into the biogeochemical cycles of C, N, and P and guidance for their impacts on ecological restoration in ecologically fragile areas.