Abstract: The retrieval of cloud microphysical properties using satellite data is crucial to not only weather monitoring and forecast but also the weather modification research. At present the main assumption for the operational retrieval of cloud microphysical properties is that only singlelayered clouds exist in the view field of the satellite. However, multilayer clouds appear very frequently. An algorithm using a combination of MODIS absorbing and nonabsorbing channels is presented for the retrieval of the optical thickness and effective particle radius of multilayer cloud, specially for cases with optically thin ice clouds overlying lower-level water clouds. Base on this algorithm the impact of the multilayer cloud that ice cloud lies over water cloud on the retrieval of cloud microphysical properties is simulated with SBDART radiative transfer model. The stimulated result shows that the error caused by considering a multilayer cloud as a single layer cloud is evident. In terms of the stimulation, an algorithm for the retrieval of the optical thickness and effective particle radius considering the effect of the multilayer cloud is presented in this paper, and a scheme is designed for the retrieval of the optical thickness and effective particle radius. In this scheme, the radiative databases of the optical thickness and effective particle radius of water cloud, ice cloud and multilayered cloud are established with SBDART radiative transfer model, considering various geometrical conditions, surface types, and atmospheric environment. After the detection of cloud mask, cloud phase and multilayer cloud, the optical thickness and effective particle radius are retrieved based on those databases, processing the channel 1 data and channel 7 data of MODIS with the method of least-squares fit. The scheme is applied to the MODIS data of TERRA on 12 July 2007, and the case study shows that our retrieval results are in good agreement with those of the MOD06 released by NASA, which indicates that the scheme is reasonable.