To overcome many defects such as the high product cost, large energy consumption, and big space capacity in conventional mechanical machining, the miniaturization of machine tool and micro factory systems has been envisioned recently. The object of this paper is to research the effect of dynamic characteristic parameters in bolted-joint beams, which is widely applied to the joining of mechanical structures in order to identify structural system characteristics and to predict dynamic behavior according to scale-down from macro to micro system as the development of micro/meso-scale machine tool and micro factories. Modal parameters such as the natural frequency, damping ratio, and mode shape from modal testing and dynamic characteristics from finite element analysis are extracted with all 12 test beam models by materials, by size, and by joining condition, and then the results obtained by both methods are compared.