Clouds have important effects on the infrared radiances transmission in that the inclusion of cloud effects in data assimilation can not only improve the quality of the assimilated atmospheric parameters greatly, but also minimize the initial error of cloud parameters by adjusting part of the infrared radiances data. On the basis of the Grapes-3D-var (Global and Regional Assimilation and Prediction Enhanced System), cloud liquid water, cloud ice water and cloud cover are added as the governing variables in the assimilation. Under the conditions of clear sky, partly cloudy cover and totally cloudy cover, the brightness temperature of 16 MODIS channels are assimilated respectively in ideal tests. Results show that when the simulated background brightness temperatures are lower than the observation, the analyzed field will increase the simulated brightness temperature by increasing its temperature and reducing its moisture, cloud liquid water, cloud ice water, and cloud cover. The simulated brightness temperature can be reduced if adjustment is made in the contrary direction. The adjustment of the temperature and specific humidity under the clear sky conditions conforms well to the design of MODIS channels, but it is weakened for levels under cloud layers. The ideal tests demonstrate that by simultaneously adding both cloud parameters and atmospheric parameters as governing variables during the assimilation of infrared radiances, both the cloud parameters and atmospheric parameters can be adjusted using the observed infrared radiances and conventional meteorological elements to make full use of the infrared observations.