Atmospheric transmittance is an important factor affecting infrared radiation transmission. The calculation of atmospheric transmittance of infrared band based on the actual meteorological parameters of marine atmospheric is still weak, which inevitably causes the calculation error. In the paper, the actual atmospheric parameter profile in coastal areas of China is constructed and embedded into MODTRAN to restore the influence of clouds cover on infrared radiation transmission in real atmospheric environment. It is found that the change of the atmospheric temperature, humidity and other parameters directly affects the calculation results of atmospheric transmittance, and the change of cloud thickness has also obvious influence on atmospheric transmittance, and its influence degree is closely related to the cloud parameters and the relative geometric position between detector and cloud layer. It is shown that to restore the real atmospheric environment as much as possible is the basis of studying infrared radiation transmission, and the error of calculation results caused by atmospheric environment cannot be ignored.