In this paper, a method of rainfall interference reduction for a Distributed Fiber Optical Intrusion Sensor System (DFOISS) is proposed and verified by experiment. The DFOISS consists of two subsystems, one of which multiplexes Continuous Wave (CW) light with pulsed light of different wavelengths of 1310 and 1550 nm to detect intrusion along the sensing fiber, and the other launches CW light to obtain a rainfall signal to reduce rainfall interference. An on-site experimental system was established to test the intrusion detection and its location in a rainy environment. The results show that DFOISS can effectively reduce rainfall interference, detecting and locating intrusion when the average number of periodic backscatter signals reaches 1,000.