We demonstrate a dual-output ultrashort pulse fiber laser with their repetition rate precisely locked. This laser source employs a mode-locked picosecond laser capable of delivering near transform-limited pulses with 21 ps duration at a repetition rate of 40 MHz. After the seed pulse is split 1∶1, it is injected into the femtosecond and picosecond pulse amplification links respectively. By effectively managing the nonlinearity and dispersion in the pulse amplification process, the synchronous output of broadband spectral femtosecond pulse and narrowband spectral picosecond pulse is realized. In the path of femtosecond pulses, a length of 50 m polarization-maintaining single-mode fiber is used to promote the spectral broadening of amplified pulses, and its spectral width is broadened to 6.12 nm owing to the effect of self-phase modulation. Then, a pair of bulk gratings is applied to de-chirp the pulse to 483 fs duration with 210 mW average power. For the other optical path, the seed pulses are firstly pre-amplified and then selected to 10 MHz repetition rate. The 200/40 photonic crystal fiber acts as the gain fiber in main amplifier to further boost the pulses, generating 25 ps pulse duration with 1.4 μJ energy and 0.86 nm spectral width. In addition, the repetition rate long-term stabilization is realized by the combination of piezoelectric translator for precise control and stepping motor for range control. When laser system warms up, the peak-to-peak fluctuation of pulse repetition rate is less than 3 mHz within 8 h, and the corresponding standard deviation is calculated to be 0.31 mHz.