In order to realize the engineering application of optical system computer-aided alignment and reach the goal of spatial location error correction for optical elements according to the misalignment by calculation, a method of transition between the misalignment by calculation and alignment quantity of adjusting mechanism is presented. Coordinate transform and least squares optimization algorithm are used to establish the misalignment-alignment quantity relation model. The coordinate datum transform between them are finished. Simulation results show that the accuracy of translational alignment quantity can reach 10-6 millimeter order and the accuracy of angular alignment quantity can reach 0.02″ order, which are calculated by self-compiled program according to the method. The accuracy of calculation is much higher than the accuracy needed for optical system computer-aided alignment. In the simulation of alignment, compared with the result of alignment on the basis of misalignment by calculation, the result of the method is much better. For different chucking methods of optical elements and adjusting mechanisms, related parameters of the method can be assigned to meet the requirements of different working conditions. The method provides the reference basis for engineering application of optical system computer-aided alignment.