An effect of thermal annealing on activating phosphorus (P) atoms in ZnO nanorods (NR) grown using a hydrothermal process was investigated. $NH_4H_2PO_4$ used as a dopant source reacted with $Zn^{2+}$ ions and $Zn_3(PO_4)_2$ sediment was produced in the solution. The fact that most of the input P elements are concentrated in the $Zn_3(PO_4)_2$ 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 $Zn_3(PO_4)_2$ particles. The solubility of the $Zn_3(PO_4)_2$ initially formed sediment varied with the concentration of $NH_4OH$. 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 $V_{Zn}$, resulting in a $P_{Zn}-2V_{Zn}$ 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.