Abstract: In this study, the secondary quadrupole ion transmission system was investigated, focusing on its design and optimization using computational fluid dynamics (CFD) and ion optics simulations. The primary aim is to elucidate the effects of airflow distribution, fringe field penetration, and operating parameters on ion transmission performance, which is crucial for improving the efficiency and resolution of mass spectrometry systems. The CFD simulations revealed that the airflow within the quadrupole system is generally stable, although significant velocity variations are observed in the inlet and outlet regions. These variations affect the overall transmission efficiency and ion trajectory. Ion optics simulations highlighted the role of the truncated quadrupole entrance in generating axial potential oscillations, whose amplitude increases as the distance between the transmission quadrupole (Q0) and the front electrostatic lens (iq0) widens. Notably, when this distance is kept below 0.476r₀, oscillations and fringe field penetration can be effectively suppressed, thereby improving ion stability and reducing transmission losses. The inclusion of a hard-sphere collision model further demonstrated that increasing the absolute value of the iq1 voltage can markedly enhance ion kinetic energy in the x-direction, reduce beam divergence, and improve focusing efficiency. The transmission efficiency remains within 84%-89% under various conditions. The performance of ions with different mass-to-charge ratios (m/z) was also simulated, revealing that the ion transmission performance was collectively determined by both ion throughput and focusing quality. The optimal performance was achieved when the Q0 radio frequency amplitude was set between 0.57 and 0.85 times that of the first-stage quadrupole mass spectrometer (Q1), thus balancing both ion focusing and transmission efficiency. These findings provide a solid theoretical foundation and engineering insights for optimizing the structural design and operational conditions of secondary quadrupole ion transmission systems. The results obtained from this study are notable for enhancing the sensitivity and stability of mass spectrometry systems. However, the current simulations focus primarily on ion transmission behavior and neglect some real-world factors, such as space charge effects and non-ideal conditions. Future work should investigate these factors and extend the model to more complex multi-stage ion optics systems. Experimental validation is also crucial to confirm the simulation results and translate these findings into practical applications for advanced mass spectrometry systems. In conclusion, this study not only quantitatively identifies key parameters for optimizing secondary quadrupole ion transmission systems but also provides practical guidelines for their design and operation. It emphasizes the importance of controlling the distance between electrostatic lenses and quadrupoles to mitigate fringe field effects, which is vital for improving ion transmission stability. These insights will be valuable for engineers and researchers working to enhance the performance of mass spectrometric instruments.