In order to investigate noise perturbation in self-similar pulse system, the variance formulae of timing and energy jitter are derived from the nonlinear Schrdinger equation with noise. Results show that the noise greatly distorts self-similar parabolic pulse shape, optical spectrum and chirp, and noise perturbation leads to pulse oscillation and frequency spectrum jitter. The pulse still has a linear chirp, but appears fluctuation at the front and back edges. The noise disturbance is very small and can be ignored in the initial stage, and the influence of noise disturbance increases rapidly with increasing of transmission distance. The influences of different dispersion and gain on time and energy jitter variances are different.