Phosphorus (P) fractionation and sorption behavior as well as the abundance and community composition of phosphorus-solubilizing bacteria (PSB) in sediments, including inorganic phosphate-solubilizing bacteria (IPB) and organic phosphate-mineralizing bacteria (OPB), were investigated in 27 sampling sites of five sections in the Three Gorges Reservoir (TGR) in December 2012. The calcium-bound phosphorus (CaCO3 similar to P) accounted for the largest part for P fractions in the sediment of TGR, which was paralleled with IPB outnumbering OPB. Furthermore, some PSB isolates, such as Micromonospora sp., Aminobacter sp., and Arthrobacter sp., were shared by the IPB and OPB. Thus, some IPB species functioned as OPB and vise versa, which could be further reflected by a negative and significant relationship between PSB (IPB + OPB) number and content of CaCO3 similar to P together with acid-soluble organic phosphorus (ASOP). Spatially, the highest ASOP content in the section Mudong and the highest CaCO3 similar to P plus iron-bound phosphorus (Fe(OOH)similar to P) as well as equilibrium phosphorus concentration (EPC0) in the sections of Yunyang and Zigui due to sediment sequestration by the dam, as well as the positive relationship between EPC0 and the ratios of different phosphorus species and phosphorus sorption maximum (Q(max)), jointly indicated pathway diversification and potential risk of phosphorus release mediated by PSB in TGR.