Considering the removal of pollutants and the resource recovery in wastewater, it is crucial to address the conflict between phosphorus pollution and phosphorus resources during wastewater treatment. This study investigated the transformation law of phosphorus in an up-flow anaerobic sludge bed reactor using different phosphorus source substrates. In addition, metagenomics sequencing was used to analyze microbial community succession and changes in the key functional genes in the reactor. Results showed that when sodium hypophosphite and sodium phosphite were used as the phosphorus sources, the average removal efficiency of total phosphorus was 6.43 % and 5.69 %, respectively. The resulting average phosphine concentrations were 109.76 mg/m3 and 72.77 mg/m3, respectively. Sodium hypophosphite was the more effective phosphorus source for Proteobacteria growth. The ppa, ppk, ppx and gcd genes were all up-regulated when exposed to the two phosphorus sources. On day 90 of the experiment, the relative abundances of these four genes in the reactor with sodium hypophosphite as phosphorus source were 0.0046 %, 0.0025 %, 0.0036 %, and 0.0014 %, respectively. In contrast, in the reactor with sodium phosphite as a phosphorus source, the relative abundances of the ppa, ppk, ppx and gcd genes were 0.0009 %, 0.0005 %, 0.0014 %, and 0.0001 %, respectively. Sodium hypophosphite was more effective than sodium phosphite in promoting the dissolution of inorganic phosphorus in microbial cells.