Quantum positioning system (QPS) is a high precision and safe positioning system. The change of photon number has a great impact on the positioning error and security. In order to reduce the positioning error and improve the safety performance of the system in rainy weather, based on the decoy state quantum key distribution protocol and the optimal average photon number adaptive (PNA) algorithm, an adaptive adjustment strategy of QPS decoy state against rainfall interference is proposed. The adaptive relationship among rainfall intensity, transmission distance and the optimal average photon number is established, and the positioning error and the security key generation rate before and after adaptive adjustment are compared. The simulation results show that when the rainfall intensity is 10 mm/h and the transmission distance is 10 km, the system positioning error decreases from 13.81 cm to 1.13 cm by using PNA algorithm. When the rainfall intensity is 1.47 mm/h and the transmission distance is 25 km, the security key generation rate of the system is improved from 5.5×10 ^-4 to 6.3×10 ^-4 by using PNA algorithm. It can be seen that the reliability of QPS in rainy weather can be improved by adaptively adjusting the average number of photons per pulse of the system.