The key to effective magnetic drug targeting (MDT) is to improve the aggregation of magnetic drug carrier particles (MDCPs) at the target site. Compared to related theoretical models, the novelty of this investigation is mainly reflected in that the microvascular blood is considered as a two-phase fluid composed of a continuous phase (plasma) and a discrete phase (red blood cells (RBCs)). And plasma flow state is quantitatively described based on the Navier–Stokes equation of two-phase flow theory, the effect of momentum exchange between the two-phase interface is considered in the Navier–Stokes equation. Besides, the coupling effect between plasma pressure and tissue fluid pressure is considered. The random motion effects and the collision effects of MDCPs transported in the blood are quantitatively described using the Boltzmann equation. The results show that the capture efficiency (CE) presents a nonlinear increase with the increase of magnetic induction intensity and a nonlinear decrease with the increase of plasma velocity, but an approximately linear increase with the increase of the particle radius. Furthermore, greater permeability of the microvessel wall promotes the aggregation of MDCPs. The CE predicted by the model agrees well with the experimental results.