The nature reserve is an important facility to protect the natural ecosystem and biodiversity, and the environmental management of the nature reserve is very important, which can ensure the protection and maintenance of the ecosystem and biodiversity of the nature reserve. The environmental management of nature reserves needs to protect the natural ecosystem, prevent human activities from damaging the natural ecosystem, maintain biodiversity and protect species diversity and ecosystem diversity. In addition, strict protection measures need to be formulated and implemented to reduce the interference of human activities to the natural environment. In short, the environmental management of nature reserves is significant for the protection of natural ecosystems and biodiversity. Therefore, this paper would optimize and design the environmental management system of the reserve through virtual simulation technology. The model construction algorithm on the basis of virtual simulation technology was used to simulate the environmental management process of natural reserves. By establishing a virtual model, the impact of different human activities on the natural environment can be simulated in order to evaluate and optimize the environmental management plan. In addition, virtual simulation technology can also help managers conduct training and simulation exercises, and improve environmental management ability and decision-making level. Experiments showed that before the implementation of environmental management, the number of cattle, sheep and deer in the nature reserve was 2214, 1865 and 1374 respectively. After the implementation of environmental management, the number of cattle, sheep and deer in the nature reserve was 2645, 2113 and 1587 respectively. Obviously, after the implementation of environmental management, the number of animals in the nature reserve has been relatively good growth, and its natural resources and ecosystem have been well protected. The experimental results showed that the virtual simulation technology can be better applied in the environmental management of the nature reserve, effectively improve the environmental management efficiency of the nature reserve, and optimize the ecosystem in the nature reserve. This result pointed out a beneficial development direction for the environmental management of nature reserves and provided reliable technical support for environmental protection.