The commonly used reference atmospheric profiles for the validation of retrieved atmospheric profiles for microwave sounders have bias compared with real atmospheric profile values, which is detrimental to the validation of the retrieval. Microwave sounder observations are the direct measurements of microwave radiation in atmospheric conditions and are a true representation of the status of the atmosphere. This paper proposed a validation method for the retrieved atmospheric temperature and atmospheric humidity profiles of the satellite-based microwave sounder using its own in-orbit observations. The validation experiments are performed both for the retrievals of the microwave temperature sounder-II (Xi’an Branch, China Academy of Space Technology, Xi’an, China. MWTS-II) and the microwave humidity and temperature sounder (National Space Science Center, Chinese Academy of Sciences, Beijing, China. MWHTS). The validation results show that the retrieved temperature profiles of MWTS-II have higher accuracy compared to the temperature profiles of ERA5 in the atmospheric pressure range of 3–30 hPa, and the accuracy of the rest of the pressure range is comparable between the profiles of ERA5 and the retrieved profiles. And the retrieved temperature profiles of MWHTS have higher accuracy compared to the temperature profiles of ERA5 in the atmospheric pressure level around 50 hPa and lower accuracy in the rest of the pressure levels. In addition, the retrieved humidity profiles of MWHTS have higher accuracy compared to the humidity profiles of ERA5 in the atmospheric pressure range of 350–925 hPa. The proposed validation method for the retrieved atmospheric temperature and atmospheric humidity profiles of MWHTS using its own observations is promising for improving the feasibility and reliability of the validation, and can be a good reference for the application of the satellite in-orbit observations and the optimization of the microwave sounders.