Soil carbon (C), nitrogen (N), and phosphorus (P) are significantly altered by vegetation succession under execution of ecological restoration projects in China. However, the changes in soil C, N, and P contents and their molar ratios as affected by vegetation succession are elusive in fragile karst ecosystems. With space-for-time substitution, this study compared the soil C, N, and P contents and their molar ratios between different vegetation successional stages in a representative karst trough valley, Southwest China. Soil samples from four positive vegetation successional stages, including herb stage (HE), hern-shrub stage (HES), shrub stage (SH), and secondary forest stage (SF), were collected to determine the topsoil C, N, and P contents and molar ratios, and selected soil physicochemical properties. The results showed that soil C and N contents increased by 158.4% and 39.6% from HE to SF, respectively, while soil P content was not significantly affected by vegetation succession. From HE to SF, soil C:N and C:P ratios increased by 82.1% and 134.2%, but soil N:P ratio vary insignificantly, respectively. Soil bulk density (BD) and pH increased but electrical conductivity (EC) decreased markedly from HE to SF. Soil exchangeable K+, Ca2+, and Mg2+ contents did not differ among four successional stages. Soil pH, BD and exchangeable K+ were closely correlated with C and P contents, C:P, and N:P in different successional stages. Our results imply that vegetation succession driven by ecological restoration considerably increases topsoil C and N accumulations but equalizes P in the karst trough valley.