Optical transfer function is widely used to evaluate the imaging performance of an optical system. Combined with confocal scanning technology, f-theta lens can increase the reading speed for microarrays greatly in guarantee of sufficient resolution and fluorescence collection efficiency, compared with micro-array analyzers that adopting mechanical scanning. In this paper, the characteristics of a confocal scanning f-theta objective lens, which was used in micro-array analyzing instrument, were analyzed by means of optical transfer function. In the whole system, laser passed through the f-theta lens, and arrived at the microarray slide where fluorophores were excited. Fluorescence emitting from the micro-array slide was collected by the same f-theta lens, and was captured by a detector. As a laser illumination system, the objective lens had a smaller stop aperture. As a fluorescence collection system, it had a bigger stop aperture. In conclusion, optical transfer function for the whole system, from source to detector, is the combination of that of the laser illumination, a coherent system, and that of the fluorescence collection system, an incoherent system. Uniformity of laser illumination at the micro-array slide was analyzed using optical transfer function during the course of scanning. The influence of aberrations on optical transfer function is given. The simulating results for above characteristics are also presented.