The Great East Japan Earthquake and the Fukushima nuclear accident cause large human population movements and evacuations. Understanding and predicting these movements is critical for planning effective humanitarian relief, disaster management, and long-term societal reconstruction. In this paper, we construct a large human mobility database that stores and manages GPS records from mobile devices used by approximately 1.6 million people throughout Japan from 1 August 2010 to 31 July 2011. By mining this enormous set of Auto-GPS mobile sensor data, the short-term and long-term evacuation behaviors for individuals throughout Japan during this disaster are able to be automatically discovered. To better understand and simulate human mobility during the disasters, we develop a probabilistic model that is able to be effectively trained by the discovered evacuations via machine learning technique. Based on our training model, population mobility in various cities impacted by the disasters throughout the country is able to be automatically simulated or predicted. On the basis of the whole database, developed model, and experimental results, it is easy for us to find some new features or population mobility patterns after the recent severe earthquake, tsunami and release of radioactivity in Japan, which are likely to play a vital role in future disaster relief and management worldwide.