To examine the effect of clamping force on the inter-layer gap formed in stacked material drilling, firstly, the drilling deformation state of stacked plates with clamping force was analyzed using elastic shell theory. Further, by finite element method, the drilling deformation model with clamping force was established in consideration of interface contact condition. The accuracy of model was verified by comparing with experimental results of single-plate deformation. Then, the changing process of inter-layer gap was analyzed under different drilling conditions. At last, the experiment was carried out to verify the finite elements analysis results. The results show that, with the increase of clamping force, the inter-layer gap will go through two stages, decreasing rapidly at first and slowly after the turning point. The turning point corresponds to the critical clamping force. To obtain an effective burr height reducing, the following two conditions must be required: Ⅰ) the inter-layer gap D_B corresponding to the turning point should be smaller than the drilling burr height without applying the clamping force, Ⅱ) the clamping force should be higher than the critical force F_B. Besides, reducing the thrust force, or minimum diameter of the clamping ring can reduce the demand clamping force and inter-layer gap size. To enhance the effects of clamping force and minimize inter-layer gap, the thicker plate and the plate with higher modules should be set as the back plate.