Monte Carlo simulation is an essential tool to assist in the design of new medical imaging devices for emission tomography. This paper modeled the full 3D whole body PET scanner and 2D animal PET scanner with septa using Monte Carlo simulation code GATE based on Geant4, analyzed the scatter fraction, scatter distribution, multiple scatter events, and scatter events from outside of FOV under 3D acquisition mode and scatter events from the septa under 2D acquisition mode. For the critical problems of 3D scatter correction: multiple scatter events and scatter events from outside of FOV, we designed additional experiments, got the fitted relationship between the percentage of multiple scatter events and the cross sectional area of the phantom, and the effects of the scatter events from outside of FOV at different ring positions; for the 2D scatter correction, we separated the scatter events from septa for analysis, and provided a quantitative reference for the elimination of these events or introduction into the procedure of reconstruction.