A confocal scanning fluorescent microscope (FCSM) changes parallel imaging, which is usually done with a conventional fluorescent microscope, to series-imaging. Because of this unique feature of imaging mean, the FCSM has the longitudinal discrimination ability a conventional fluorescent microscope does not have. The imaging principles of a FCSM are described briefly. Through an established mathematical model of system transfer function, the depth resolutions are calculated numerically. In biology science, the aberrations are introduced when an oil-immersion objective is used to study thick specimens, such as tissues and living cells, whose reflective indexes are significantly different from that of the immersion oil used in the experiment. Finally, after numerical calculation, a set of optimization curves for compensating the aberrations are given graphically under the different conditions, the compensation method proposed in this paper is suitable both for oil-immersion and non- immersion objectives.