According to the development of tool material and the improvement of machinability of cutting material like aluminium alloy, the higher spindle speed is needed. However, the higher speed causes the heat generation of bearings, the deformation of spindle unit parts, and the rotational accuracy of spindle to be worse. Therefore, it is essential to analyze and control the heat generation and the thermal behavior of spindle unit in order to have higher speed and better rotational accuracy. This paper shows the analogy between the analyzation of heat generation and thermal behavior of high speed spindle system by finite element method and the test results of actual temperature rise through running test, and shows the necessity of cooling the spindle and inner ring side of bearings for the thermal balance of high speed spindle system.