This paper focuses on addressing the challenges of low gain and poor gain uniformity in side-window dynode photomultiplier tubes (PMTs). Using CST software for simulation, the study proposes an optimization approach based on three-dimensional dynamic simulation technology. By constructing a highly accurate simulation model, the influence of multiple structural parameters-including photocathode position, dynode shape, arrangement angle, spacing, and length-on the gain performance of the PMT is systematically analyzed. Furthermore, visualized electron trajectory tracking technology is utilized to intuitively demonstrate the effects of different structural configurations on electron motion paths and gain behavior.The side-window PMT model developed in CST retains the core components critical to gain performance, including the grid mesh, cathode, nine-stage dynodes, and anode. The surfaces of the dynodes are coated with high secondary electron emission materials, which emit secondary electrons under bombardment by incident electrons. The entire model operates in a vacuum environment. In the simulation, photoelectrons emitted from the cathode under the influence of an electric field strike the dynode surfaces, exciting secondary electrons. These secondary electrons, driven by the electric field gradient, repeatedly collide between the dynodes and undergo successive multiplication, eventually reaching the anode, where they are absorbed to generate an output electrical signal. The proposed simulation approach has been validated through the design and development of several PMTs, confirming its reliability. Previous applications of this method have successfully contributed to the design of other types of PMTs that have been implemented in practical production.The study shows that optimizing the relative angle between the photocathode and dynodes improves electron collection efficiency, increasing it to 77%. Modifying the dynode shape (e.g., optimizing it to an arc shape) and adjusting its curvature can further focus the electron trajectories, significantly enhancing dynode gain performance. Additionally, optimizing the spacing and length ratio of the dynodes is critical to improving overall gain: when the spacing is set to 7.5 mm, the gain reaches its maximum; when the length ratio of the dynode to cathode is optimized to 1.4, gain loss is minimized. Through these structural optimizations, the PMT gain increases from an original value of 9.1×10⁶ to 2.1×10⁷ without altering the dynode material or operating voltage.In summary, the study demonstrates that in the design of side-window PMTs, adjusting the angle between the grid mesh and the photocathode, as well as modifying the electric field distribution among the cathode, grid mesh, and dynodes, can more effectively guide photoelectrons emitted from the cathode to be collected by the dynodes, thereby enhancing the overall gain of the PMT. The variation in dynode shape leads to differences in the electric field distribution between dynodes, which subsequently affects the trajectories of secondary electrons emitted by the dynodes. Arc-shaped dynodes, in particular, are shown to have the potential to partially focus electron trajectories. By adjusting the curvature of the arcs, the positions at which secondary electrons bombard the next-stage dynodes can be altered, enhancing the electron collection efficiency of the dynodes and effectively increasing the PMT gain.For cage-structured dynode arrangements, when the shape and voltage distribution of the dynodes are fixed, there exists an optimal spacing between dynodes. This optimal spacing arises due to changes in the electric field intensity between the dynodes, which influence the impact positions of the electrons on subsequent dynodes. Additionally, photoelectrons emitted from the edges of the cathode are less likely to be collected by the dynodes. Optimizing the length ratio between the cathode and dynodes is shown to improve the cathode's sensitivity and the overall gain of the PMT.In conclusion, the proposed simulation and optimization methods provide a systematic framework for improving the design and performance of side-window PMTs. The significant gain improvements achieved through these optimizations underscore the potential for broader application of these design principles in the development of next-generation photomultiplier tubes.