Abstract: Femtosecond lasers with high repetition rates play important roles in advanced manufacturing, such as high-speed laser ranging and three-dimensional imaging. Among them, high-order harmonic mode-locking based on femtosecond fiber lasers is one of the important methods to obtain high repetition rates above GHz. Based on a nonlinear polarization rotation (NPR) mode-locked Ytterbium (Yb) fiber laser with dispersion compensation from intra-cavity grating, a stable 143 MHz fundamental frequency mode-locked pulse sequence was obtained when the pump light was 180 mW. When the pump power was increased to 1 W, the highest 20th harmonic (2.86 GHz) mode-locked pulse train was obtained. The Allen deviation and phase noise of the output pulse repetition rates of the Yb fiber laser were studied systematically when it was running at high harmonic mode-locking and fundamental mode-locking respectively. The repetition frequency locking accuracy can be maintained at a stability of 10⁻¹³ Hz@1 s in the 7th harmonic mode locking state. This study provides an experimental basis for high harmonic mode-locked femtosecond laser pulse sequence to be used for precise measurement.