Soil C:N:P stoichiometry plays a vital role in nutrient cycling in ecosystems, but its importance to P transformation in paddy soil remains unclear. We investigated the effect of soil C:N:P stoichiometry on P mobility and uptake under long-term fertilization. Three treatments, CK (no fertilization), NPK (inorganic nitrogen, phosphorus and potassium fertilization) and NPKM (combined inorganic NPK fertilizer and manure application), were selected from two long-term experiments of paddy soil that were initiated in 1991 and 1982 in Chongqing and Suining, respectively. The results showed that in comparison the control treatment, under long-term fertilization, soil pH decreased. In comparison with the NPK and CK treatments, the NPKM treatment significantly increased soil nutrient contents, P uptake and phosphatase activities. In comparison to the CK treatment, the NPK and NPKM treatments significantly decreased soil C:N, C:P and N:P ratios. In comparison to NPK and CK treatments, the NPKM treatment decreased residual-P at both sites. Compared with CK treatment, the NPKM treatments increased labile-P and moderately labile-P by 987% and 144%, respectively, and NPK treatment increased these factors by 823% and 125%, respectively, at the Chongqing site. At the Suining site, with NPKM treatment, increases in labile-P and moderately labile-P were 706% and 73%, respectively, and with NPK treatment, the increases were 529% and 47%, respectively. In contrast, non-labile-P was significantly decreased with NPKM treatment in comparison to that with NPK and CK treatments. Moreover, increases in soil C:N and C:P ratios decreased the labile-P pools and increased non-labile-P pools. A path analysis indicated that soil C:N:P stoichiometry indirectly controlled P uptake by directly affecting P transformation from non-labile to labile-P pools. Moreover, the non-labile-P in soil with high SOM and P content directly affected P uptake, indicating that soil P transformation is mainly driven by soil C and P in paddy soil. In conclusion, understanding mechanism of P mobility influenced by soil C:N:P stoichiometry could be helpful to manage soil P fertility under long-term fertilization in paddy soils of these regions.