By taken the threeaxis micro milling machine driven by linear motor as an object of study, the surface integral method was used to calculate each main joint surface parameters of the machine tool. Two kinds of overall finite element model (FEM) for modal analysis were established respectively with and without consideration of the influences from junction surface. The modal testing system of micro milling machine was set up, and the experimental modal analysis was completed. The experimental results show that the junction surface of parts influences a lot to the modal of the machine. The results of the test and modal analysis are almost the same with consideration of the influences from junction surface, and the maximum error is 81%, which verifies the rationality and validity of the overall FEM. On basis of this, the overall harmonic response analysis is completed. The analysis results indicate that the maximum dynamic displacement of the spindle at bottom is 12 μm, which meets the design requirement of a machine tool basically.