The purpose of this paper is to estimate thermal deformation of machine tool model by using transfer function with time delay. The prediction method of thermal deformation based on frequency domain is constructed from transfer function between specified surface temperatures and the relative displacement in cutting area. The relative displacement in cutting area is predicted using two specified surface temperatures near heat source in machine tool model. As a result, the method can be predicted with enough certainty at what rate the temperature changes the most rapidly on machine's startup transient behavior. The method proposed in this paper is remarkably effective to estimate thermal deformation and confirm that the error between experimental and estimated values will be remarkably reduced.