Low-carbon agriculture is a new farming production mode, is the new application of low-carbon economy in the farming field, low-carbon agriculture has multiple functions such as farming safety production, farming climate regulation, farming ecological conservation and promoting rural financial development. The development of low-carbon agriculture is on the green innovation of agriculture, but the development of green agriculture is still in the preliminary exploration stage, and the growth rate is slow. Therefore, how to scientifically construct development mechanism of green agriculture and reveal its economic effect is the key problem to promote healthy and steady development of green agriculture in our country at present, which has the very important theoretical and practical significance to develop modern agriculture and promote ecological civilization construction. This research is based on industry life cycle, infant industry, ecological agriculture and mechanism design theories. Then, based on farming carbon emissions, green GDP nuclear the results were combined with the panel data from 2019 to 2022 to evaluate the performance of green innovation systems in eastern, western, northeastern and central China, and analyze their spatial differences and temporal variations. Through the convergence verification analysis, it is found that the overall convergence rate of the country is 3.2%, while in the regional area, the convergence rate of the eastern part is 12.9%, and the western part is 5.3%. This shows that the low efficiency areas in the west are catching up with the high efficiency areas in a rapid growth way, and the differences between the regions are shrinking.