Variable pitch end mills are widely used in the high-speed milling process due to having better vibration reduction properties. However, because of the unequal pitch angles and the asymmetrical structure of end mills, there are principle error, poor dynamic balance accuracy, and serious tool vibration problems in the milling process. In order to improve the dynamic balance accuracy of variable pitch end mills, the structure of the end mill is designed and optimized based on the minimum eccentricity criterion in this paper. Firstly, by analyzing the dynamic balance of variable pitch end mills, the relationship between it and eccentricity is defined, and the end section model and the centroid equation are developed through the structure design of end mills. Then, the optimization method of variable pitch end mills is analyzed, the eccentricity decreases from e0= 150um to e'0 = 3um based on this method. the structure of the end mill is optimized to meet the design criteria, which improves the balance accuracy level of end mills. Finally, through the modal analysis for the optimized structure of the variable pitch end mill, the maximum relative displacement in the mode is reduced by about 17%, it is verified that the optimized end mills have better dynamic performances, which is of great significance for alleviating the cutting vibration and improving the cutting stability.