In this paper, the modulation transfer function with aberration of a multichannel laser induced fluorescence analyzer is presented. Based on an f-theta lens, the confocal system was used both to transform the exciting laser and to collect the fluorescence emitted from sample. The total MTF is the combination of that of both systems. A simple method for the numerical calculation of that was also given. From the calculating result we could conclude that the aberration had poor impact on the MTF of a confocal multichannel fluorescence analyzer and the imaging performance was uniform in the full field.