The laser transmission quality will be affected if the surface of ultra-smooth optical component of laser system is polluted. In order to reduce the contamination deposition, the study on characteristics of contaminant deposition on ultra-smooth optical surface is of great significance. In this paper, the samples treated by different means are tested by atomic force microscope and Fourier infrared spectrometer. The results show that the deposition of contamination is increasing with the increase of time. This kind of contaminant might contain -NH chemical bond, which will cause the change of roughness of the ultra-smooth optical surface, also, it can be effectively removed by cleaning with alcohol, acetone or chromic acid, or by means of plasma discharge in oxygen atmosphere. However, high temperature baking has no obvious effect on the elimination of contaminant. This result is considered that the possible cause of surface contamination on the ultra-smooth optical component in vacuum system is the slow release of the residual organics during the process of optical component processing. Therefore, for ultra smooth optical elements with extremely high cleanliness requirements, auxiliary materials that are easy to be eliminated by organic solvent are suggested to be used as much as possible during the processing process, and the storage time should be reduced after processing, which can effectively improve the cleanliness of optical elements.