The development of informatization impacts all sectors, including agriculture. Agricultural informatization builds the knowledge linkage structures of agricultural innovation systems globally. This study investigated the global knowledge linkage structures in agricultural innovation pertinent to information technology (IT) for agricultural research and development (R&D) investments and activities. We explored the longitudinal trend of systemness within the networked research relationships in the triple helix (TH) of the university, industry and government (UIG). We collected data from publications in the Science Citation Index (SCI), the Social Sciences Citation Index (SSCI), and the Arts and Humanities Citation Index (A&HCI) to analyze the TH network dynamics. We also performed a scientometrics analysis to quantitatively identify the knowledge and insights of global agricultural innovation structures. These results could be informative for individual countries. Our findings reveal that the global knowledge linkage structures in the agricultural sector that are pertinent to IT fluctuate widely and fail to increase the capacity of agricultural innovation research due to a neglect of the network effects of the TH dynamics of UIG.