Obtaining temperature and humidity profiles with high vertical resolution is essential for describing and predicting atmospheric motion, and, in particular, for understanding the evolution of medium- and small-scale weather processes, making short-range and near-term weather forecasting, and implementing weather modifications (artificial rainfall, artificial rain elimination, etc.). Ground-based microwave radiometers can acquire vertical tropospheric atmospheric data with high temporal and spatial resolution. However, the accuracy of temperature and relative humidity retrieval is still not as accurate as that of radiosonde data, especially in cloudy conditions. Therefore, improving the observation and retrieval accuracy is a major challenge in current research. The focus of this study was to further improve the accuracy of atmospheric temperature and humidity profile retrieval and investigate the specific effects of cloud information (cloud-base height and cloud thickness) on temperature and humidity profile retrieval. The observation data from the ground-based multichannel microwave radiometer (GMR) and the millimeter-wave cloud radar (MWCR) were incorporated into the retrieval process of the atmospheric temperature and relative humidity profiles. The retrieval was performed using the backpropagation neural network (BPNN). The retrieval results were quantified using the mean absolute error (MAE) and root mean square error (RMSE). The statistical results showed that the temperature profiles were less affected by the cloud information compared with the relative humidity profiles. Cloud thickness was the main factor affecting the retrieval of relative humidity profiles, and the retrieval with cloud information was the best retrieval method. Compared with the retrieval profiles without cloud information, the MAE and RMSE values of most of the altitude layers were reduced to different degrees after adding cloud information, and the relative humidity (RH) errors of some altitude layers were reduced by approximately 50%. The maximum reduction in the RMSE and MAE values for the retrieval of temperature profiles with cloud information was about 1.0 °C around 7.75 km, and the maximum reduction in RMSE and MAE values for the relative humidity profiles was about 10%, which was obtained around 2 km.