In order to reduce the white noise and pulse noise in the acceleration signal of civil engineering structural health monitoring, a combinative method of medial filter and wavelet threshold is proposed. Because of the decomposition level has a significant impact on the result of denoising, in order to get a better denoisng result, a self-adaptive method to select the decomposition level is proposed , the method to determine the value of threshold on each level is also been given in this paper. The analysis of numerical simulation and the on-site measured data from the structural health monitoring system of National Aquatics Center of Beijing 2008 Olympic venues shows that, the method proposed in this paper can overcome the defect of wave threshold method which doesn’t have obvious effect to reduce the pulse noise, it can reduce the white noise and pulse noise at the same time, provide data of higher signal to noise ratio for modal parameter identification and so on.