Under the special background of China, the cooperative innovation between different government-industry-university-research institutes plays an increasingly important role in the agricultural field. However, the existing literature has paid little attention to it. Considering the cooperation patents, published in the agriculture field stemming from the Full-text Database of China Patents as the study object, the spatial and institutional attribute of the authors as the data source, and by combining the social network and spatial econometrics analysis, this paper analyzes the structure evolution characteristics of cooperative innovation networks of agricultural government-industry-university-research institute in the city level of China in 1985–2014, based on the triple helix theory, with the influence factors discussed. This shows that, 1) since 1985, China's agricultural innovation level has been substantially increased, but the development degree of the cooperative innovation network is low, and the patent cooperation mainly relies on authors in the same unit; 2) enterprises play a leading role in the agricultural cooperative innovation. The effect of the government and hybrid organizations driven by the government is not obvious; 3) the cooperative innovation in the province and city dominates, and a multi-pole pattern has been formed. The cooperative innovation network structure evolves from a single helix empty core and double helix multi core to a double helix hierarchical network; 4) the city's science, education funding and personnel investment are key factors determining the agricultural cooperative innovation, while the agricultural development of the city presents slight negative impacts on it. The spatial mismatch of supply and demand is present in the technical cooperative innovation of China's agriculture. Therefore, the science enhancement and education investment to big agricultural provinces should be promptly implemented.
