In order to research the influence of layer thickness fluctuations on the performance of quasi-fractal photonic crystal filter and to find out the tolerance of the thickness fluctuations, the influence of layer thickness fluctuation on the filter properties of quasi-fractal photonic crystal filter containing negative material is analyzed through adding different thickness fluctuations both in positive and negative refractive index layers. Laws of the transmission peak shifting with the refractive index, number of the layers and the thickness of layer fluctuation are summarized. The statistic figures of the positions of the transmission peaks are simulated and the statistic feature of the position of the transmission peaks are analyzed when the random geometric thickness fluctuations are added in each layer. The conclusion is that the tolerance of random geometric thickness fluctuation of this kind of photonic crystal filter used in dense wavelength dovision multioplexing (DWDM) optical communication system is only 0.01 nm.