Accurate and stable in-orbit radiometric calibration of a satellite instrument is fundamental to Earth geophysical parameter estimation. This article addresses the intercalibration of the microwave temperature sounder (MWTS) on the Chinese second-generation polar-orbiting meteorological satellite, Fengyun 3D (FY-3D), against the advanced technology microwave sounder (ATMS) aboard the Suomi National Polar-orbiting Partnership (S-NPP) satellite. First, ocean and land microwave radiative transfer models (RTM) are constructed by combining the sea and land surface emissivity models and atmospheric absorption model, as well as the intercalibration equations. Then, the MWTS and ATMS observations are resampled into a 1° × 1° regular grid space, and the matching brightness temperatures (TBs) under clear-sky/near clear-sky conditions are collected. Next, the TBs at top-of-atmosphere are simulated using the RTM and the fifth generation of European Centre for Medium-Range Weather Forecast atmospheric reanalysis (ERA5) data. After that, the double differences between FY-3D MWTS and S-NPP ATMS and the theoretical observations in FY-3D MWTS channels are calculated. Finally, the radiometric calibration coefficients of FY-3D MWTS are successfully derived from the observations of S-NPP ATMS by linear fits on the matching TBs. In contrast to the ATMS measurements, FY-3D MWTS observations are generally overestimated, and the in-orbit radiometric calibration errors (mean ± standard deviation at the mean) are 1.83 ± 1.45, 0.45 ± 0.94, 1.87 ± 0.60, −0.20 ± 0.36, −0.02 ± 0.37, 0.19 ± 0.24, 1.69 ± 0.28, 2.25 ± 0.29, 1.97 ± 0.33, 1.74 ± 0.42, 2.84 ± 0.42, 0.07 ± 0.65, and 0.32 ± 1.18 K in FY-3D MWTS channels 1–13, respectively. The results with Hewison's semi-empirical land surface emissivity (LSE) model and the results with LSEs derived from the coincident ATMS observations at 50.3 GHz are consistent. Moreover, the intercalibration results obtained by the RTM in this work also agree well with the results obtained by the community radiative transfer model.