With the development of the electronics industry, the requirements for chips are getting higher and higher, and thinner and thinner wafers are needed to meet the processing of chips. In this study, a model of the adhesion state of semiconductor wafers in the stacking–clamping process based on microarray adsorption was established, the composition adhesion was discussed, the microarrays of different materials and pressures were experimentally studied, and a molecular dynamics model was established. The molecular dynamics analysis showed that the adhesion force was only related to the type of atom, and the applied pressure did not change the adhesion force. According to the simulation results, the tangential adhesion between the metal and the wafer is greater than that between the ceramic and the wafer, the adsorption force between the aluminum–magnesium alloy and the silicon wafer is shown in the normal direction, and the repulsion force between other materials and the silicon wafer is shown in the normal direction. During the pressure process, the metal is in the elastic deformation stage between the metal and the wafer, the wafer is plastically deformed in the silicon carbide ceramic and wafer, and the wafer is elastically deformed in the alumina ceramic and wafer. In this paper, the adhesion between the substrate and the wafer is studied, a method of constructing microarrays to enhance adhesion is proposed, and the tangential deformation of the array unit under pressure is studied, which provides theoretical support for increasing the adhesion by constructing microarrays.