With the development of Industry 4.0, hard-cut materials such as titanium alloys have been widely used in the aerospace industry. However, due to the poor rigidity of titanium alloy parts, deformation and vibration easily occur during the cutting process, which affects the accuracy, surface quality and efficiency of part machining. Therefore, in this paper, tool runout and workpiece deformation are introduced into the milling process of flat-end mills. Based on the tool’s hypocycloid motion, a geometric parameter model of the milling process is established, and the undeformed cutting thickness model is obtained considering the tool runout and workpiece deformation. Finally, the milling force model for side-milling titanium alloy thin-walled parts was established. The accuracy of the force model is verified through experiments. The error of the proposed model is far less than that of the traditional basic method. The maximum error of the traditional basic method is 87.09%. However, the maximum error of the proposed model is only 66.54%. The results show that the proposed force model considering tool runout and workpiece deformation can provide more accurate milling force prediction.