The FE model of a combined gantry milling machine was constructed. The joint stiffness of bolt fastening, ball screw, and roller guideway were calculated. The static analysis, modal analysis and harmonic analysis of the whole machine were carried out. The results indicated that the static stiffness and minimum dynamic stiffness of the spindle could satisfy the accuracy requirements of milling, but the stiffness of the X-axis feed system was comparatively low, while the stiffness of the rest and the cross-beam could be relatively abundant. The result of “considering joint stiffness” modal analysis was more accurate than “unconsidering joint stiffness”, especially the 5th-order natural frequency had a difference of up to 52.2%. The harmonic analysis result showed that the response amplitude of the spindle center was comparatively large in three directions when the 1st-order and the 17th-order natural frequency were working, so the frequencies should be avoided while working.