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Long-term repetition frequency stabilization of passively mode-locked (ML) fiber lasers using high-frequency harmonic synchronization is investigated. First, the standard cavity length controlling-based stabilization scheme is studied mathematically, and its disadvantages in high-frequency harmonic synchronization are analyzed. Theoretical studies are then carried out to prove that by modulating the pump power of lasers, the disadvantages can be overcome, and high-stability stabilization with low noises can thus be achieved. Based on the studies, an improved frequency stabilization scheme for passively ML fiber lasers is proposed. Its performances are evaluated by synchronizing a high-frequency harmonic of an ML laser with a 3.035-GHz reference microwave signal. Results show that the residual phase noise for the stabilization (synchronization) reaches around -100 dBc/Hz (-120 dBc/Hz) at 3-Hz (10 KHz) offset frequency, which results in 14.9 fs (21.2 fs) timing jitter integrated from 1 Hz to 0.1 MHz (1 MHz). The long-term (2 h) phase drift is less than 12 fs for in-loop measurement. For out-of-loop measurement, the drift is ~74 fs, while the measurement setup itself brings a drift of ~55 fs. The research provides deep studies for frequency stabilization of passively ML fiber lasers and can benefit their applications in various areas.