There are some problems in the design of three-dimensional visualization teaching resources, such as less involved in interactive design, no unified design standards, the lack of effective innovation guidance mechanism and no unified evaluation system. Based on the design principle, taking amino acids as an example, this paper proposes a design plan for 3D visualization resources in teaching scenarios. According to the design scheme, the three-dimensional visualization resources are made. The main processes include the selection of the tools, the preparation and production of the material, the writing of the script, the design of the learning interface, the design of the interactive logic relationship and the control and output of the program. Finally, the three-dimensional visualization resources are used in the future classrooms with starC electronic double board and group touch screen, and the results are analyzed and evaluated. It is found that the three-dimensional visualization resources can effectively improve the students' interest in learning and help students understand knowledge.