Efficient design on the molecular and crystal levels is an urgent need to accelerate the development of energetic materials (EMs), and the performance analysis of microstructures is the most important thing in the research and design of EMs. Although molecular simulation methods are widely used in various research fields, there are few comprehensive reviews on analytical techniques. It is urgent to understand the basic principles of various analytical methods in the research of EMs. In this article, the characterization/analysis methods in quantum mechanics and molecular mechanics simulation technology are summarized, and their applications in the field of EMs are listed. At the molecular level, energy, composition, geometric structure, and electronic structure are all related to macroscopic properties, and most of them have been widely used as variables in numerical models to predict and compare the properties of EMs. In addition, this paper emphasizes that the correlation between theoretical calculation and confirmatory experiment needs to be further verified because the current experimental characterization can also be dealt with by molecular simulation, which is helpful to the popularization and application of theoretical research.