New energy materials are materials that support the development of new energy, have energy storage and conversion functions, or materials that integrate structure and function. This material can increase the investment and operation of new energy systems. The focus is mainly on the research process of material design through physical research. The proposal of this technology can save the use of non-renewable resources, and its performance exceeds the traditional meaning. New energy is mainly based on new technologies and new materials to make energy renewable, and through utilization and development, limited resources can form a cycle. This article aims to study the use of computer simulations and the design of organic functional molecules for new energy materials, observe the difference between new energy materials and traditional materials through these two technologies, and obtain their characteristics through the analysis of this new energy material. The analysis of these theories is finally applied to practice. In this article, a related introduction to a process and design of computer simulation is proposed, and then combined with the analysis of organic functional molecules, through the derivation of formulas and related data, the motion properties of the relevant molecules of new energy materials are obtained, and the new energy materials are further understood. Energy materials, through quantification and data presentation, it can be concluded from experiments and analysis that the molecular tension of new energy materials is related to various factors.