Atmospheric temperature, water vapor, surface skin temperature and surface emissivity are the intrinsic information of the atmosphere and surface of earth. Retrieval of atmospheric temperature profile and water vapour profile is important for accurate weather forecasting and climate change research by using satellite infrared data, at the same time, the retrieved surface skin temperature and surface emissivity spectra were used to study the growth of plant and crop yield, evaporation and circulation of surface water, energy balance, surface composition and physical properties, climate change and global environment. In this paper, considering the atmosphere and the ground as a whole system, the retrieval method for simultaneous retrieval of atmospheric temperature profiles, water vapour profiles, surface emissivity, and surface skin temperature was established. simultaneous retrieval were performed by using hyperspectral infrared satellite Atmospheric Infrared Sounder data (AIRS) in China’s Xinjiang region for two typical desert and snow features. Firstly, infrared radiation transmission equation of earth-atmosphere system was linearized. Then, it was proposed that atmospheric profile and surface emissivity can be structured by Empirical Orthogonal Functions (EOF) to effectively reduce the inversion variables. The physical simultaneous retrieval algorithm could be developed finally. In the retrieval process, the first guess values were obtained through National Centers for Environmental Prediction (NCEP), and the optimum solution could be obtained by Newton iteration method. The observation area covered the Taklamakan desert and Junggar basin in Xinjiang, China. The latitude of the Tazhong observation station is 38.98 degrees and the longitude is 83.64 degrees, which is located in the hinterland of the Taklimakan desert in central tarim basin. The latitude of National field science observation station of fukang desert ecosystem is 44.2 degrees and the longitude is 87.9 degrees, which is located in Junggar basin. The Tazhong observation station and National field science observation station of Fukang desert ecosystem were selected to be the retrieval of the ground verification point. These stations were selected to be the retrieval of the ground verification point. The results showed that the surface temperature in the Taklamakan desert is significantly higher than that in Junggar basin, which is consistent with the actual situation. According to the retrieval of the surface emissivity distribution at 8.6 and 13.4 μm, it could be seen that the desert surface emissivity is significantly lower than the emissivity of snow at 8.6 μm, and retrieval of the two kinds of ground infrared emissivity spectrum is consistent with the laboratory measurement of emissivity spectra by comparing the retrieved surface emissivity and the jet propulsion laboratory measurement of desert and snow emissivity data between 6～15 μm. The atmosphere and ground were considered as a whole system, the surface emissivity was added in the retrieval in this paper. Through comparison and analysis of retrieved two kinds of ground atmospheric profile with the local meteorological sounding values and traditional method retrieval, the research showed that the retrieval accuracy of atmospheric temperature and water vapour profile is improved, especially the improvement is obvious in the boundary layer. At the same time, the analysis showed that the improvement of the retrieval precision of the atmospheric profile in the desert region is higher than that in the snow region. Because the surface emissivity changes within the spectrum is larger in the desert area, while the surface emissivity changes within the spectrum is smaller in the snow area. It is important that using the proposed approach can simultaneously retrieve atmospheric temperature profiles, water vapour profiles, surface emissivity and surface skin temperature. The retrieval precision of the atmospheric temperature profile and water vapour profile in the desert area can be improved more effectively compared with snow region. This paper can provide the service and support for the numerical weather forecast and the future hyperspectral infrared satellite application in China, which is of great significance.