Abstract: The irradiation throughout means the amount of the cells irradiated per unit time, which is the important performance indicator of a single ion microbeam system. To improve the single ion localization irradiation throughout, microfluidic chip technology is applied to the single ion beam cell irradiation system with single ion to single cell auto-irradiation. A cell storage pool, O₂ and CO₂ injection channels, constant temperature control, pH detection and cell inspection are built on the chip. Ions irradiate the moving cells through the irradiation point on the microfluidic chip. Based CAS-LIBB system, this article establishes a computational model for ion targeting microfluidic cells. The basic methods and laws of ion targeting microfluidic cells are studied, therefore it has obtained the multi-relationships among cell velocity, irradiation throughout, irradiation dose, and cell separation, which are the theoretical guidance for system operation. A mode of “Promptly Irradiate with Inspected” is proposed to improve the irradiating effectivity and accuracy. The results show that there is an upper limit for cell speed as well as for irradiation throughout, and increasing cell number density and ion emission density are the most feasible ways to raise the irradiation throughout. With the microfluidic technology, the irradiation throughout now reaches 10000 cells/h, more than 10 times higher than before. The calculated data is basically consistent with the experimental results.