To set up a practical identification system for agroecology is a key step to push forward agroecology to be widely recognized and accepted by the public. It is also a precondition for government to make supporting policy and market development for agroecology products. This article proposes that the identification principle for agroecology should follow the bottom line that farming practices are compatible with its resources, conserving and protecting its eco-environment and guarantee for food safety. The farming methods adopted for agroecology should be very inclusive. They may screen and integrate from traditional wisdom, farmers’ practices, scientific research results and high-tech innovations. The operational standard for identifying agroecology need a unified principle nationwide, but a locally specified index. When making the identification index system, it should be noticed that there are different views for agroecology farming on farm size, owner type, farming methods used, farm impacts, and change in social management. The identification system should be formed according to the bottle neck problems locally faced, the key methods to solve them, and the key status appeared after solving them in the region. The credit recording system and information technology should be used to increase the efficiency of the identification system. There are advantages and disadvantages in both the third-party certification method and the participatory guarantee system. The identification system for agroecology should adopt different approaches to accelerate the process, hence to accelerate the development of market and government policy for agroecology.