Environmental protection in Yunnan Province is related to local sustainable development, and has a regional or even international significance. During the 11th National Five-Year Plan, positive progresses had been made in the environmental protection in Yunnan Province. However, there are still some critical challenges, including conflicts between economic development and environmental protection, contamination reduction, pollution transferred from the provinces of east China and environmental protection issues arcross nations. Facing serious issues such as execrable water environment, soil pollutions of heavy metals, rural environmental pollution, biodiversity loss, invasion of the alien species and weak environmental supervision ability of the local governments, it is urgent to take active measures to adjust the industrial components from the point of environmental management and improve the economic development styles. It is necessary to strengthen the water pollution control of the drinking water sources and the critical watersheds, the air pollution control especially on reducing the emission of sulfur dioxide and nitrogen oxides, and the prevention and control of the pollutions caused by solid wastes focusing on handling with hazardous waste. It is also important to pay special attention to the issues on biodiversity conservation and prevention and control of soil heavy metal pollution, improve the capacity of environmental risk prevention, innovate environmental management policies and mechanisms, enhance the construction of environment supervision capacity and improve the overall level of environmental management.