AbstractThe presence of clouds greatly disrupting the estimation of observation errors in satellite data. Therefore, cloud detection is a necessary step in satellite radiance data assimilation, not only to identify clear sky data and cloudy data, but also, more importantly, to accurately specify observation errors in different scenarios during all‐sky data assimilation. However, the assimilation of the microwave temperature sounder‐2 (MWTS‐2) onboard the FengYun‐3D satellite has been restricted by the low accuracy of cloud detection due to the absence of low‐frequency channels, especially for land areas where complex underlying surface brings more difficulties to the identification of cloudy data. The microwave humidity sounder‐2 (MWHS‐2), which is designed for water vapor sounding, is usually equipped on the same satellite as MWTS‐2. The sensitivity of the MWHS‐2 to water vapor enables it to provide more accurate information about clouds over land. Based on the advantage of the two instruments measuring on the same platform, an effective cloud detection method for MWTS‐2 data over land is established in this study after collocating the data of the MWTS‐2 and MWHS‐2. The results show that the new method achieves a cloud detection rate exceeding 75%, with a significantly reduced false detection rate compared with the traditional scattering index method, which is decreased from 40% to approximately 26%. More importantly, in non‐precipitating cloud regions, the cloud index built by the new method has a significant linear correlation with the difference between observed and simulated brightness temperatures (OMB) of MWTS‐2 data. Statistical analysis reveals that the cloud index can be used to effectively rectify the systematic OMB bias caused by those clouds in non‐precipitation cloud areas, which demonstrates the promising application of this cloud index in all‐sky MWTS‐2 data assimilation over land.