An error evaluation method for the opto-mechanical system of a large aperture telescope was proposed based on structure function. The error transfer property of the structure function was analyzed, and the numerical simulation of the atmosphere disturbance was obtained by inverting the Power Spectral Density(PSD). Then, the error allocation of opto-mechanical system was built with the structure function consequently. The method was proved to be correct and feasible with the application in the 1.23 m telescope in the Changchun Institute of Optics, Fine Mechanics and Physics. Finally, the method was used in the tertiary mirror system of 30 m telescope(TMT), and the print through effect of the system in the atmosphere disturbance was researched. The experiment show that the resolution ability of the system for print through peaks does not weaken at different seeings. The method proposed has important significant for reducing the cost efficient of the large aperture telescope and lowering its risk in developing and use processing.