The different remote sensors on China new generation meteorology satellite FY-3 have similar thermal infrared channels. For the visible and infrared radiometer (VIRR) infrared 4-channel and medium resolution spectral imager(MER- SI) infrared 5-channel, the line-by-line radiative transfer model (LBLRTM), in which the atmospheric profiles adopt glob- al 52 atmospheric profiles generated by ECMWF, was performed to calculate the spectral radiance emitted from the earth-at- mosphere between 8μm and 14μm. The radiance received by the satellite was computed combined with the spectral re- sponse functions of channels and then the theoretical relationship of the brightness temperatures for the two channels was an- alyzed. The FY-3 actual observation data at QingHai Lake in September 2008 was used to examine the relationship. The comparison of the results indicates that the brightness temperatures for both channels calculated by LBLRTM agree each other well, but the temperature obtained from MERSI is lower than that from VIRR. The temperature difference between the two channels increases with the increase of temperature. Because FY-3 actual observations are affected by many factors, VIRR temperature is lower than MERSI, which is different from the theoretical result of the model. The matched MODIS data is used to compare with MERSI and VIRR. It is concluded that VIRR might underestimate the temperature. The deviation of MODIS and MERSI temperaturesis within the absolute accuracy of the temperature measurements. The results described here should be valuable for assessing the similarities and differences for the two similar infrared channels of MERSI and VIRR.