In the image deconvolution of digital confocal microscopy system, the selection of spatial size of three dimensional point spread function (3D-PSF) is closely related to the effect of image restoration. Based on the principle of three- dimensional microscopic imaging and 3D- PSF model, the relationship between the energy distribution and the size of 3D-PSF is analyzed, and a 3D-PSF size selection method is proposed and realized, which uses the restoration efficiency - energy curve inflection point for energy threshold determination. The acquisition of image and the generation of 3D-PSF of bio-optical microscope objective of three kinds of numerical aperture or magnification are simulated, and the deconvolution restoration results of three-dimensional simulated cell images by using the 3D-PSFs with different energy are obtained. The experimental results show the effectiveness and feasibility of the proposed method, and provide a basis for automatic selection of 3D-PSF for the three-dimensional microscopic image deconvolution.