It is often difficult to achieve further optimization results of machine tool parts in terms of sizes parameters after the topology structure of these parts are determined. Taking the machine bed structure of a horizontal machining center as an object, a twolevel optimization method of the unit structure was proposed, which was based on the analysis and optimization of unit structure, to optimize the whole machine tool bed. Firstly, according to structural features of this machine tool bed, different unit structures were analyzed and compared, and then the round and oval sand hole with original sizes parameters were chosen as the most suitable units to redesign the bed structure. After that, based on response surface method and taking the whole machine tool bed as optimization goal, the secondlevel optimization of unit structure in terms of sizes parameters was achieved. On the premise of minimal change of bed mass, the results of the analysis demonstrate that the twolevel optimization method achieves better dynamic performance of machine tool compared with singlelevel optimization method which only focuses on the optimization of unit structure. To be more specific, the former method can increase the fundamental frequency of this machine tool bed 3 times than the latter method. Besides, when the former method is applied, the biggest resonance peak of this machine tool is reduced by 55.2% in Xdirection, 83.9% in Ydirection, and 82.8% in Zdirection.