Abstract: With the rapid development of space optics technology, high-performance space optical payloads raise higher requirements for the mitigation of molecular contaminations. It is necessary to carry out simulation analysis of molecular contamination transmission and deposition at the initial stage of payload design, so as to provide better feedback and to guide payload design. In view of the time-consuming feature of conventional Monte Carlo method to deal with complex structures when simulating space molecular contamination, an innovative simulation analysis on molecular contamination transmission and deposition in space based on gas diffusion equations was carried out to obtain the distribution data of contamination deposited on the sensitive lens in this work. The contamination effects were also investigated by ground experiments and the results indicated that molecular contamination can lead to an attenuation of 5.3% in the optical performance of sensitive lens after three years in orbit. The results may provide some guidance for the design and development of space optical devices.