The phase noise in the 100 Hz-1 kHz band of erbium-ytterbium co-doped single-frequency fiber amplifier was studied, and it was proved by experiments that the peak noise was the phase noise produced by the pump power supply. Based on the power transfer equations of erbium-ytterbium co-doped fiber amplifier and the heat transfer function of pump laser, the effects of pump power, pump wavelength and gain fiber length on the phase noise in 100 Hz-1 kHz band were analyzed numerically. The phase noise of the output laser was measured by using two-stage optical amplifier structure, and the experimental results were compared with the numerical simulation results, which proved the reliability of the theoretical model. This study optimized the phase noise characteristics of erbium-ytterbium co-doped single-frequency fiber amplifier with main resonance power amplifier structure and provided guidance for improving beam combining efficiency in coherent combination. In general, the aforementioned findings hold true for fiber amplifiers with main oscillation power amplification structure.