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We analyze the environmental effect on the standard phase-locking of the mode-locked laser. The mechanism of the improved phase-locking loop (PLL) with a standard proportional-integral-derivative (PID) regulator is described, and its stabilization principle is analyzed in detail. We utilized the standard PLL and the PLL with a standard PID regulator to phase-lock a mode-locked erbium-doped fiber laser to a rubidium atomic clock at 100 MHz for days. The agreement between the experimental results and simulation has proved that our theoretical analysis for phase-locking of mode-locked laser with PID regulator is correct. The phase-locking experiment also shows that the PLL with PID regulator has a good performance of long-term phase and frequency stabilities.