High precision locking of the repetition rate of a semiconductor saturable absorber mirror mode-locked all polarization maintaining fiber laser is achieved by using the method of resonance-enhanced nonlinearity in an additional active fiber. A 980/1064 nm wavelength division multiplexer (WDM) and a piece of Er-fiber are added in the fiber cavity to induce the change of nonlinear refractive index and optical cavity length. By feedback controlling the pump power of LD2, the refractive index of the Er-fiber is modulated, and thus the optical length of the laser can be controlled to achieve the high precision locking of the repetition rate. The length of the Er-fiber and the initial pump power of LD2 are optimized to maximize the range and precision for repetition rate locking. Results show that as much as 180 Hz controlling range is obtained in the condition of 1.75 m length of Er-fiber. The repetition rate of locking accuracy is just closely related to the initial pump power and is not significantly affected by the length of Er-fiber. The range of repetition rate peak-to-peak is less than 0.5 mHz, the corresponding standard deviation is 0.16 mHz, and the standard deviation of output power is 0.009 mW in the condition of 18 mW pump power of LD2. Moreover, the pump power of LD1 is controlled by the feedback, when removing Er-fiber and the WDM. Due to the superposition of the resonance-enhanced nonlinearity and the Kerr nonlinearity on the refractive index of Yb-fiber, the repetition rate increases to 1 kHz with a slightly decrease of locking accuracy in a stable single pulse mode locking range.