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The High Energy Cosmic Radiation Detection (HERD) facility will be installed on the China space station, and the critical sub-detector is the homogeneous, isotropic, and finely segmented 3D calorimeter (CALO), composed of 7500 LYSO cubes. In this paper, GEANT4 was used to simulate the optical photon propagation inside a single LYSO crystal including the Wavelength Shifting Fiber (WLSF) and photodiode (PD) and compared with experimental results. The results show that only a tiny fraction of the photons produced in the LYSO can be collected through the WLSF and PD, and the light output can be enhanced by increasing the number of rough surfaces. Additionally, the variability in WLSF and PD light output when particles entered the LYSO crystal from varying positions, known as non-uniformity, was examined through simulation. The simulated non-uniformity using thin X-ray beams is compatible within the experimental errors and can be improved at higher light output. Finally, the non-uniformity is highly sensitive to the polishing condition of the crystal surface, and better polishing conditions are preferred. [ABSTRACT FROM AUTHOR]