A high-resolution frequency shift measurement based on the time domain mode-locked optoelectronic oscillator (TDML-OEO) is proposed and experimentally demonstrated. In the proposed approach, the TDML-OEO is firstly excited and the central frequency is selected by injecting a reference microwave signal through an electrical coupler (EC) and used as the reference frequency measurement comb. Then a named unknown microwave signal with various and lower up to even 1 Hz shift compared to the reference microwave signal is injected into the TDML-OEO loop. Due to such a small frequency difference, the central frequency and nearby sidebands will have spectrum aliasing with the reference signal, which is very difficult to be distinguished by low resolution spectrograph. Benefiting from the comb effect, the small frequency difference is enlarged by fine controlling the loop delay time. The proposed method displays high resolution and accuracy due to the comb effect, which will find potential usage in the Doppler radar system for ultra-slow target detection.