Recently, the world has witnessed the most severe pandemic (COVID-19) in this century. Studies on epidemic prediction and simulation have received increasing attention. However, the current methods suffer from three issues. First, most of the current studies focus on epidemic prediction, which can not provide adequate support for intervention policy making. Second, most of the current interventions are based on population groups rather than fine-grained individuals, which can not make the measures towards the infected people and may cause waste of medical resources. Third, current simulations are not efficient and flexible enough for large-scale complex systems. In this paper, we propose a new epidemic simulation framework called HMES to address the above three challenges. The proposed framework covers a full pipeline of epidemic simulation and enables comprehensive fine-grained control in a large scale. In addition, we conduct experiments on real COVID-19 data. HMES demonstrates more accurate modeling of disease transmission up to 300 million people and up to 3 times acceleration compared to the state-of-the-art methods.