In order to evaluate the long term stability of opto-mechanical systems, a novel method of long term instability evaluation based on the calculation of misalignment is presented. Firstly, a model has been built to find the relationship between the misalignment of the opto-mechanical systems and the wavefront error with the aid of sensitivity matrix, and a method for the misalignment calculation based on singular value decomposition (SVD) is given. Then, a reduced projection system is illustrated to analyze the relationship between the aberration singular vector and the configuration singular vector base on the SVD of constructed sensitivity matrix. Intended misalignments are added to the actual reduced projection system and the calculated result verifies the availability of the method. Finally, the long term stability is tested and it can orientate the opto-mechanic optimization.