Higher education institutions serve as the primary platform for cultivating innovative talents, and experimental teaching is a key means of training students to adapt to social development. This study developed and implemented a self-designed virtual simulation project under the experimental courses of biochemistry and molecular biology. By studying the advanced management system of the national biological experimental teaching center, we optimized our center's management system by introducing and supplementing regulations in multiple aspects, including bio-safety management. Thus, a scientific and efficient management system is formed and applied in practice. Then, establish a detailed schedule for the use of experimental instruments, improve the supporting resources of equipment, form a precise usage mode of instruments and equipment, and ensure the safety and standardization of teachers and students during the usage process.