A diaphragm pump is a type of volumetric pump that has excellent sealing performance. An electromagnetic diaphragm pump is a kind of widely adopted diaphragm pump that has a simple structure, low power loss, and high cost performance. However, the calculation method of deformation for the electromagnetic diaphragm pump rubber diaphragm is presently lacking. Herein, a calculating method of deformation for the electromagnetic diaphragm pump rubber diaphragm is proposed. By establishing and analyzing a deformation model of the electromagnetic diaphragm pump rubber diaphragm, a theoretical relationship between the deformation of the electromagnetic diaphragm pump rubber diaphragm, the size of the electromagnetic diaphragm pump rubber diaphragm and the pressure of fluid is determined. The experimental results indicate that the biggest difference between the tested axial deformation and the calculated axial deformation of the electromagnetic diaphragm pump rubber diaphragm is 0.04 mm and the calculation results show agreement with the experimental results.