The difficulty of getting medical treatment is one of major livelihood issues in China. Since patients lack prior knowledge about the spatial distribution and the capacity of hospitals, some hospitals have abnormally high or sporadic population densities. This paper presents a new model for estimating the spatiotemporal population density in each hospital based on location-based service (LBS) big data, which would be beneficial to guiding and dispersing outpatients. To improve the estimation accuracy, several approaches are proposed to denoise the LBS data and classify people by detecting their various behaviors. In addition, a long short-term memory (LSTM) based deep learning is presented to predict the trend of population density. By using Baidu large-scale LBS logs database, we apply the proposed model to 113 hospitals in Beijing, P. R. China, and constructed an online hospital recommendation system which can provide users with a hospital rank list basing the real-time population density information and the hospitals' basic information such as hospitals' levels and their distances. We also mine several interesting patterns from these LBS logs by using our proposed system.