Abstract: In order to study the noise perturbation in self-similar pulse systems, we derive the variance of timing jitter and energy jitter from the nonlinear Schrodinger equation. The numerical results show that the noise greatly distorts self-similar parabolic pulse shape, optical spectrum and chirp. The noise perturbation leads to pulse oscillatory and frequency fluctuant. Although the chirp still reveals linear, undulation appears at both edges. The noise perturbation effects obviously increase if distance extending while they can be negligible in the initial stage. The normal GVD and gain play different roles on the variance of timing jitter and energy jitter. Keywords: noise perturbation, the variance of timing jitter, the variance of energy jitter