An in-depth understanding of the soil nutrient status and balance relationship can help the effective recovery and management of alpine degraded meadows. In order to study the balance relationship among soil carbon, nitrogen, and phosphorus nutrients during the heavy degradation stage of meadows, field sampling and investigation, indoor analysis, and mathematical statistics were used to explore the characteristics and driving factors of changes in soil carbon, nitrogen, and phosphorus content, storage, and ecological stoichiometry during the heavy degradation stage of alpine meadows in the Sanjiangyuan region. The results showed that in the heavy degradation stage, miscellaneous grass plants occupied absolute dominance, soil C∶N∶P was approximately 32.83∶3.87∶0.67, and there was certain nitrogen limitation. The coefficients of variation of soil carbon, nitrogen, and phosphorus content were in the following order: organic carbon (1.09) > total nitrogen (0.63) > total phosphorus (0.29). The organic carbon content and the carbon and nitrogen ratio showed a significant linear decreasing trend with the increase in the grassland degradation index (GDI), while the total phosphorus content and organic carbon storage showed a significant non-linear change, in which the total phosphorus content showed a significant gentle U-shaped distribution, and the organic carbon storage decreased more gently at the beginning of the heavy degradation stage and then decreased sharply when the GDI was 57.9. The results of Mantel correlation analysis showed that the soil carbon to nitrogen ratio, carbon to phosphorus ratio, and nitrogen to phosphorus ratio showed significant correlation with organic carbon content and storage and total nitrogen storage. The results of structural equation modeling indicated that soil water content had direct effects as well as indirect through vegetation factors, soil carbon, nitrogen, and phosphorus ecological stoichiometry ratios, and soil water content and vegetation factors (height, cover, and biomass) were key environmental factors affecting soil ecological stoichiometry. The research results can provide scientific basis and practical guidance for the restoration of heavily degraded grassland in alpine meadows.