An effect of thermal annealing on activating phosphorus (P) atoms in ZnO nanorods (NR) grown using a hydrothermal process was investigated. NH4H2PO4 used as a dopant source reacted with Zn2+ ions and Zn3(PO4)2 sediment was produced in the solution. The fact that most of the input P elements are concentrated in the Zn3(PO4)2 sediment was confirmed using an energy dispersive spectrometer (EDS). After the hydrothermal process, ZnO NRs were synthesized and their PL peaks were exhibited at 405 and 500 nm because P atoms diffused to the ZnO crystal from the Zn3(PO4)2 particles. The solubility of the Zn3(PO4)2 initially formed sediment varied with the concentration of NH4OH. Before annealing, both the structural and the optical properties of the P-doped ZnO NR were changed by the variation of P doping concentration, which affected the ZnO lattice parameters. At low doping concentration of phosphorus in ZnO crystal, it was determined that a phosphorus atom substituted for a Zn site and interacted with two VZn, resulting in a PZn-2VZn complex, which is responsible for p-type conduction. After annealing, a shift of the PL peak was found to have occurred due to the unstable P doping state at high concentration of P, whereas at low concentration there was little shift of PL peak due to the stable P doping state.