China is facing increasing challenges in food security and environmental protection, and the plant breeding has made enormous contribution to solving the problems. The legal protection of new plant varieties has the important function of encouraging innovations in the field of plant breeding. However, the widely use of modern biotechnology has caused great controversy in society, and some people propose to limit the scope of plant variety right, especially for Genetically Modified Organisms (hereinafter “GMOs”). When designing and interpreting the regulations on the protection of new plant varieties, we should keep in mind that the plant variety right is a private right aiming to encourage innovation, and take the principles and relationships in the field of innovation into consideration. Proper regulation and incentives for innovation are both the essential themes in the fields of modern technologies. Intellectural property (hereinafter “IP”) laws should focus on encouraging innovation, while the law system, including the Seed Law, the Food Safety Law and the Environmental Protection Law, should provide systematic, scientific and strict regulations on the research, propagation and marketing of new plant varieties. The whole law system and the market can function together to guide the plant breeders to be committed to breeding new varieties that meet the needs of food security, food safety and environmental protection.