A dynamic model for the over-hang part of the micro-endmill is proposed, which comprehensively considered the shear deformations and rotary inertia effect arising from the nature of the micro-endmill by using the theory of Timoshenko beam. The convergence behavior of the built model is analysed, and its accuracy is verified by experiment, and the applicability of the model is proved by comparing with the calculated results from finite element method and the Euler beam theory. Based on the developed model, the effect of the tool tip diameter, tip section aspect ratio and semi-taper angle on the natural frequencies of micro-endmill are studied. The proposed model enables better parametric design and optimization of micro-endmill for excellent dynamic performance.