In order to reduce the machining deformation of thin-walled parts during milling, a non-uniform allowance planning method for thin-walled parts based on workpiece deformation constraint with the idea of adding materials in reverse material removal sequence is proposed in this paper. Firstly, a cutting force threshold calculation method is proposed according to the finite element method. The cutting force threshold at different positions is calculated by obtaining the local stiffness characteristics at the cutter-contact (CC) point under the constraint of allowable deformation. And then, the maximum machining allowance at the CC point is calculated depending on the cutting force model. Considering that the stiffness of the workpiece is position-dependent and affected by material removal, the stiffness of the workpiece is updated by adding elements in the reverse cutting direction, and the stock of finishing is obtained by surface fitting. Experimental results show that compared with the traditional uniform allowance method, the error of the proposed method is reduced by about 83%, which can effectively reduce the deformation and improve the machining accuracy.