Gain-parameter-dependent transfer functions and phase-noise performances in a mode-locked Yb-doped fiber laser are measured in this study. It is discovered that the corner frequency in the amplitude and phase domains is determined by the absorption coefficient of the gain fiber, when the total absorption and other cavity parameters are fixed. This shows that an oscillator using gain fiber with higher dopant concentration accumulates more phase noise. Furthermore, we present net cavity dispersion-dependent transfer functions to verify the effect of dispersion management on the frequency response. We derive a guideline for optimizing mode-locked fiber laser design to achieve low phase noise and timing jitter.