To satisfy the requirements of five-axis processing quality, this article improves and optimizes the machine tool structure design to produce improved dynamic characteristics. This study focuses on the investigation of five-axis machine tools’ static and dynamic stiffness as well as structural integrity. We also include performance optimization and experimental verification. We use the finite element approach as a structural analysis tool to evaluate and compare the individual parts of the machine created in this study, primarily the saddle, slide table, column, spindle head, and worktable. We discuss the precision of the machine tool model and relative space distortion at each location. To meet the requirements of the actual machine, we optimize the structure of the five-axis machine tool based on the parameters and boundary conditions of each component. The machine’s weight was 15% less than in the original design model, the material it was subjected to was not strained, and the area of the structure where the force was considerably deformed was strengthened. We evaluate the AM machine’s impact resistance to compare the vibrational deformation observed in real time with the analytical findings. During modal analysis, all the order of frequencies were determined to be 97.5, 110.4, 115.6, and 129.6 Hz. The modal test yielded the following orders of frequencies: 104, 118, 125, and 133 Hz. Based on the analytical results, the top three order error percentages are +6.6%, +6.8%, +8.1%, and +2.6%. In ME’scope, the findings of the modal test were compared with the modal assurance criteria (MAC) analysis. According to the static stiffness analysis’s findings, the main shaft and screw have quite substantial major deformations, with a maximum deformation of 33.2 µm. Force flow explore provides the relative deformation amount of 26.98 µm from the rotating base (C) to the tool base, when a force of 1000 N is applied in the X-axis direction, which is more than other relative deformation amounts. We also performed cutting transient analysis, cutting spectrum analysis, steady-state thermal analysis, and analysis of different locations of the machine tool. All of these improvements may effectively increase the stiffness of the machine structure as well improve the machine’s dynamic characteristics and increases its machining accuracy. The topology optimization method checks how the saddle affects the machine’s stability and accuracy. This research will boost smart manufacturing in the machine tool sector, leading to notable advantages and technical innovations.