Digestate of rural animal manures (DM) contain valuable P resource, but when they are directly used on land, they can cause soil and water pollution. Hydrothermal treatment (HT) has been widely applied as an effective method of waste treatment and P recycling. This study aims to realize the P recovery in DM by illustrating the migration and transformation of phosphorus (P) species during HT process of DM. Two acids (e.g., hydrochloric acid and oxalic acid) were compared in terms of their abilities to extract P from solid products after HT process. The results revealed that organic phosphorus (OP) was converted into inorganic phosphorus (IP), whereas non-apatite phosphorus (NAIP, mainly AlPO4) was transformed to apatite phosphorus (AP, Ca3(PO4)2) during HT at different temperatures. Specifically, the percentage of IP increased from 30.4% in DDM to 90.6% after HT process at 220 °C (HT220). The P leaching efficiency of HT220 reached 94.8% during HCl extraction. The study indicated that P bioavailability and solubility could be improved by HT process. This study would provide deeper insights into the application of HT technology for recovery of P in DM, as well as provide guidance for P recovery and recycling from P containing wastes.