Abstract: As an independent sand control unit or a common protective shell of a high-quality screen, the punching screen is the outermost sand retaining unit of the sand control pipe which is used in geothermal well or oil and gas well. However, most screens only consider the influence of the internal sand retaining medium parameters in the sand control performance design while ignoring the influence of the plugging of the punching screen on the overall sand retaining performance of the screen. To explore the clogging mechanism of the punching screen, this paper established the clogging mechanism calculation model of a single punching screen sand control unit by using the computational fluid mechanics-discrete element method (CFD-DEM) combined method. According to the combined motion of particles and fluids, the influence of the internal flow state on particle motion and accumulation was analyzed. The results showed that (1) the clogging process of the punching sand control unit is divided into three stages: initial clogging, aggravation of clogging and stability of clogging. In the initial stage of blockage, coarse particles form a loose bridge structure, and blockage often occurs preferentially at the streamline gathering place below chamfering inside the sand control unit. In the stage of blockage intensification, the particle mass develops into a relatively complete sand bridge, which develops from both ends of the opening to the center of the opening. In the stable plugging stage, the sand deposits show a “fan shape” and form a “V-shaped” gully inside the punching slot element. (2) Under a certain reservoir particle-size distribution, The slit length and opening height have a large influence on the permeability and blockage rate, while the slit width size has little influence on the permeability and blockage rate. The microscopic clogging mechanism and its law of the punching screen prevention unit are proposed in this study, which has some field guidance significance for the design of punching screen and sand prevention selection.