Linear motors generate high heat and cause significant deformation in high speed direct feed drive mechanisms. It is relevant to estimate their deformation behavior to improve their application in precision machine tools. This paper describes a method to estimate its thermal deformation based on updated finite element(FE) model methods. Firstly, a FE model is established for a linear motor drive test rig that includes the correlation between temperature rise and its resulting deformation. The relationship between the input and output variables of the FE model is identified with a modified multivariate input/output least square support vector regression machine. Additionally, the temperature rise and displacements at some critical points on the mechanism are obtained experimentally by a system of thermocouples and an interferometer. The FE model is updated through intelligent comparison between the experimentally measured values and the results from the regression machine. The experiments for testing thermal behavior along with the updated FE model simulations is conducted on the test rig in reciprocating cycle drive conditions. The results show that the intelligently updated FE model can be implemented to analyze the temperature variation distribution of the mechanism and to estimate its thermal behavior. The accuracy of the thermal behavior estimation with the optimally updated method can be more than double that of the initial theoretical FE model. This paper provides a simulation method that is effective to estimate the thermal behavior of the direct feed drive mechanism with high accuracy.