As a second generation of China's polar orbiting meteorological satellite, the satellite of FY-3A and FY-3B were launched in 2008 and 2010, sequentially, in sun-synchronous orbits located at the altitude 831 km. The FY-3A/B load totally 11 sensors, including microwave sensors, such microwave temperature sounder (MWTS), microwave humidity sounder (MWHS) and microwave radiometer imager (MWRI), etc. In this paper, based on atmospheric radiative transfer model, intercalibration of multi-channel MWRI measurements with, correspondingly, AMSR-E data are analyzed. Some FY-3B MWRI data along Yangtze River area during spring and summer seasons of 2011 are specifically collected. Based on radiative transfer and MWRI features, the polarization indexes for monitoring drought and flooding happened during those periods are quantitatively analyzed and compared by AMSR-E data. Meanwhile, the scattering indexes are also analyzed for monitoring rainfall, and validated by AMSR-E data and ground station records.