To ensure the alignment accuracy of wing in aircraft assembly, an evaluation algorithm is proposed, which is based on tolerance constraints. With relative deviation of wing-fuselage joints and level-measuring points, an evaluation function of assembly errors is constructed. The optimization model of wing digital alignment is established to minimize the synthesis assembly error with tolerance requirements, which are made of 3D tolerance of wing-fuselage joints and relative tolerance between level-measuring points. The non-linear constrained optimization problem is solved by Lagrange multiplier method and quasi-Newton method and its initial value is provided by SVD method. The optimized position and orientation of wing is obtained, which makes the tolerance requirements be met and the synthesis assembly error minimal. Compared with the result of SVD method through simulated data, the algorithm is validated.