For the spindle vibration during working process of the SH50 electrical discharge machining (EDM) machine tool, the modal characteristics of the spindle combining theoretical analysis with experimental verification are studied. First, the finite element model is built in ANSYS Workbench, and the theoretical modal of the spindle is analyzed. Further, the weak links in the spindle are found out during working process by testing its operating deflection shapes (ODS). Then, based on the effective independence method and modal assurance criterion (MAC) matrix, the sensor placements of key parts are optimized before modal experiment. After that, the modal and ODS tests are carried out on the spindle head according to the result of sensor placements optimization. At last, some advices on spindle vibration reduction are put forward after confirming the theoretical model by the experimental results. The simulation result shows that adding a backboard can greatly reduce the vibration of the spindle.