A scheme of equalizing the uneven pulse amplitude from a rational harmonic mode-locked laser is proposed and verified, in which an optical fiber active ring filter is employed. The active ring filter is a comb filter with tunable free spectral range, which can select the mode-locked component and suppress other harmonics and super-modes by carefully tuning the optical delay line in it. This process is able to effectively balance the pulse amplitude. Theoretically, the simulation is performed to compare the waveform and radio frequency spectrum before and after filtering. The results show that the active ring filter can effectively filter the expected frequency, and the higher the Q is, the better the amplitude equalizationisis. In the experiment, the 7th, 11th, 14th mode-locked pulses are verified respectively and mode-suppression ratio can be improved by more than 20 dB.