To explore soil nutrients and their ecological stoichiometry characteristics under six ecosystems including farmland (ST), dry land (HD), grassland (CD), shrubbery (GC), plantation (RGL) and secondary forest (CSL)), were studied in karst canyon region by a combination of field investigation and laboratory analysis. The results showed that: (1) soil nutrient content under six ecosystems had a decreasing trend with soil depth except total potassium (TK), while the verse was true for soil pH. (2) Compared with the global soil average level, the ratios of carbon to nitrogen, carbon to phosphorus, carbon to potassium, phosphorus to potassium, and nitrogen to phosphorus ratio in six ecosystems were low in the karst canyon region. (3) Both soil nutrients contents and stoichiometry significantly differed among six ecosystems and soil fertility presented in the order of secondary forest > plantation > farmland> dry land > shrubbery > grassland. The main influencing factors varied at different developing stages and under different ecosystems; thus, respective management and fertilization measures should be adopted to promote vegetation restoration and rapid ecological reconstruction in the karst canyon region and even the whole southwest karst area of China.