River ice in the upper Yarlung Zangbo River is characterized by seasonal freezing-thawing cycles (SFTC). It is important to explore the effects of SFTC on phosphorus release and transformation from upstream surface sediments to protect the ecosystem of the Yarlung Zangbo River. The process and mechanism of phosphorus release and transformation in sediments following SFTC were investigated in a laboratory simulation experiment. The results showed that after freezing, sediment particles were broken, the specific surface area was increased by 14%, and the particle size was decreased by 43%, which resulted in weakened adsorption of phosphorus by sediments. Moreover, the destruction of organic matter (OM) on the sediment surface will release more ion adsorption sites and promote the release of phosphorus. The bioavailabilities of exchangeable phosphorus (Ex-P), aluminum phosphorus (Al-P) and iron phosphorus (Fe-P) increased by 60.09%, 86.86% and 31.86%, respectively, after freezing. Organic phosphorus (O-P) is used indirectly by organisms, and O-P content showed a significant correlation with OM content. Water affected the oxygen content in sediments during the freezing period, and continuous hypoxia promoted the release and transformation of Fe-P and Al-P.