Reflection of the rise f agro-food production costs is analyzed based on the introduction of the quality safety situation of agricultural products in China . Firstly, rise of production cost caused by the demarcation of prohibited areas; secondly, rise of production cost caused by using environment-friendly agricultural inputs; thirdly, rise of production cost caused by quality control; rise of production cost caused by product certification. The ecological compensation mechanism which is beneficial to agro-food quality safety is set up according to the principle “the one who is benefited compensates”. Firstly, laws and regulations of agricultural production compensation are to be actively perfected. Secondly, experience of developed countries can be borrowed to establish a fiscal transfer payment system of production compensation. Thirdly, ecological agriculture is to be developed to produce products with safety and high quality. Since agro-ecological compensation can make up for the cost paid for protecting agro-ecological environment and producing safe agro-products by agro-food producers, and is beneficial to arousing producers’ motivation, compensation is made for agriculture producers from compensation objects, compensation scope and compensation mechanism to improve the quality safety level of agricultural products.