Monte Carlo simulation plays an important role in the study of time of flight (TOF) positron emission tomography (PET) prototype. As it can incorporate accurate physical modeling of scintillation detection process, from scintillation light generation, the transport of scintillation photos through the crystal(s), to the conversion of these photons into electronic signals. The Geant4 based simulation software GATE can provide a user-friendly simulation platform containing the properties needed. In this work, we developed a dedicated module in GATE simulation tool. Using this module, we simulated the light yield, energy resolution, time resolution of LYSO pixels with the same cross-section ($4\times4 mm^{2}$) of different lengths: 5 mm, 10 mm, 15 mm, 20 mm, 25 mm, coupled to a PMT. The experiments were performed to validate the GATE simulation results. The results indicate that the best time resolution (484.0$±$67.5 ps) and energy resolution (13.3$±$0.4 %) could be produced by using pixel with length of 5 mm. The module can also be applied to other cases for precisely simulating optical photons propagating in scintillators.