A significant size effect will occur on the tool part of micro-end mill due to its small diameter, which means the internal structure of the tool part material will affect the mechanical properties of the tool part. In view of this, a comprehensive method considering size effect is proposed in this paper to predict both the static and dynamic behaviors of micro-end mill more accurately. Based on the strain gradient elasticity theory (SGET) and Hamilton’s principle, dynamic model of micro-end mill tool is presented, in which the Timoshenko beam model (TBM) considering the shear deformations and rotary inertia effects is employed. Based on the presented model, the static and dynamic behaviors of micro-end mill is obtained utilizing the finite element method (FEM). The influences of size effect on micro-end mill are investigated in detail by contrasting the static and dynamic behaviors of micro-end mill with different tool diameters and different length-to-diameter ratios, respectively. In order to verify the accuracy and efficiency of the presented method, an improved experiment is performed in this paper.