Green development is a new mode to solve the contradiction between agricultural development and ecological protection in the new era. It is very urgent to improve agricultural green development level of the restricted development zones because of its special status in safeguarding national agricultural products and ecological security for countries worldwide. From a new perspective of agroecosystem symbiosis, this study makes dynamic comparative analysis of agricultural green development level between 2013 and 2018 by constructing multi-dimensional evaluation index system from green production, green innovation, green eco-protection and green economy. The results indicated that: (1) on the whole, the agricultural green development level in Yili River Valley shows an upward trend, but that of most counties belong to the low-and medium-level; (2) the spatial heterogeneity of agricultural green development are more obvious, showing the characteristics of high in the northwest and low in the southeast; (3) by clustering analysis with the comprehensive evaluation matrix of green agriculture, there exist three types of agricultural development: “High level-High benefits”, “High level-Low benefits” and “Low level-Low benefits”, presenting an unbalanced development state. On this basis, according to the existing problems and the advantages for development of Yili River Valley, this study proposed the green empowerment path of agro-ecosystem symbiosis based on protecting ecological chain and promoting value-added chain, which has broad prospects for promotion and application in similar restricted development areas.