With the application of finite element method on structure design and engineering analysis more and more widely, this paper presents a response surface model hybrid artificial bee colony method to optimize the thermal boundary conditions in finite element thermal analysis of a machine tool spindle to improve its finite element simulation precision. Initially, the thermal experiment and finite element thermal analysis of the machine tool spindle with initials that were calculated by empirical formulas were conducted, respectively. Additionally, focusing on thermal boundary conditions, a response surface model is designed to establish the explicit expression between thermal boundary conditions and the simulation errors; then, an artificial bee colony algorithm is used to solve the mixed-variable optimization problems of a response surface model. Finally, the optimized thermal boundary conditions are brought into the finite element method of a machine tool system, and the simulation accuracy has been greatly improved.