Supercontinuum sources via femtosecond pumping in highly nonlinear photonic crystal fibers considerably impact scientific research and industrial applications. Herein, we investigate the complex transfer function of relative intensity noise in a broadband fiber supercontinuum source generated using an ytterbium-doped mode-locked laser. A designed intensity noise was artificially added to the system through the introduction of weak sinusoidal intensity modulation to the seed pulses. Owing to the influence of nonlinear gain dynamics and soliton dynamics during power amplification and spectral broadening, the transfer functions exhibit unique frequency and wavelength dependencies. Systematic measurements indicate that the seed transfer functions exhibit the characteristics of damped high-pass filters and saturate at low Fourier frequencies within the fiber amplifier. Moreover, supercontinuum broadening induces a nonlinear transformation of fluctuations, resulting in considerable amplification and negative correlation within the dispersion wave and soliton self-frequency shift regions. Clarifying the mechanism and bandwidth of this system is imperative to achieving low-noise supercontinuum generation because they provide insights into the nonlinear laser dynamics associated with broadband spectral broadening and noise transformation.