In pigeon farming, manure cleaning is predominantly manual, a method that is both slow and costly, and exposes workers to harsh conditions. Addressing these challenges, this paper introduces a cleaning robot for pigeon farms utilizing magnetic strip navigation combined with RFID signal recognition and derives the magnetic-navigation control model. This method can improve operational stability and accuracy. Given the farm’s unstable environment, a control algorithm based on fuzzy PID with Kalman filtering was developed. This algorithm mitigates input disturbances and measurement noise by integrating Kalman filtering into the fuzzy PID feedback loop, thereby refining signal accuracy. Numerical simulations conducted in Matlab/Simulink demonstrate that the inclusion of Kalman filtering reduces the time of target signal tracking by nearly 1 s compared to fuzzy PID and by almost 2 s relative to standard PID under identical disturbances. Experimental tests confirm that this algorithm significantly improves the robot’s operational stability and reduces magnetic-navigation deviation, underscoring its advancement and practicality over traditional PID and fuzzy PID methods.