The thermal deformation of a machine tool spindle influences the performance of the manufacturing systems for precision products. In this research, thermal analysis of a high speed machine tool spindle with the rolling bearing and the built-in motor is carried out by using Finite Difference Method. The thermal boundary conditions describing the heat generation in the bearing and built-in motor are considered in the simulation. And various convective boundary conditions are assumed with the empirical formula in the references. From the simulation results, the characteristics of each element affecting the dynamic thermal behaviour of the machine tool spindle system have been clarified. Therefore, this model can be well applied to the future development of the high speed spindle systems.