Microchip capillary electrophoresis (CE) has been recognized as a powerful tool for biochemical analyses due to its micro size, fast separation and low sample requirement. According to the characters of CE signal, the Db12 wavelet with a level decomposition of 5 and the thresholding method of sqtwolog-hard were conformed as the optimum denoising strategy after computations. The result shows that, using this strategy, simulated capillary electrophoresis noise could be removed adequately. Compared with Fourier transform denoising method, discrete wavelets transform (DWT) is an efficient method for noise removal with a better preservation of the spiky shapes of CE signal