Optical coherence tomography (OCT) and confocal scanning microscopes can perform three dimensional (3D) optical imaging of target objects. They are widely used in many fields because of their non-contact measurement, real-time fast imaging and high resolution. This paper is dedicated to evaluating the resolution of 3D optical imaging systems, enabling third-party metrology assessment, assuring periodic quality, and comparing different systems. An improved standard test method based on the system 3D point spread function (PSF) is proposed in this paper. The standard diameter microspheres were embedded in the robust PSF phantoms as scattering particles. An OCT and a confocal scanning microscope were used to acquire the 3D PSF images. Different from previous studies, this paper proposes a new preparation process for PSF phantoms. In addition, new mathematical model was built based on statistical methods to analyze the PSF that includes hundreds of scattered data. Combining the imaging principles of OCT and confocal microscopy, the imaging resolution of the two optical systems was compared. Finally, a stability experiment was performed to further verify the feasibility of using the PSF to evaluate the resolution performance of the imaging system. The results showed that the resolution based on PSF analysis is in good agreement with the theoretically calculated value, and this method can be used to reliably evaluate the resolution of 3D optical imaging system in the future.