Most of the knowledge-based economies (KBEs) operate in a neoclassical economic model that does not recognize the importance of natural resources and sustainability beyond the market forces. In contrast, KBEs that rely on endogenous factors harmonize with the enlightened anthropocentrism for sustainable development with scientific and technical abilities to design the ecological system for infusing human values into nature. For example, the Quintuple Helix Model of Innovation. In this exploratory research, it was found that the conventional structure of universities in Botswana is unable to produce glocal green knowledge and innovation in their mainstream knowledge production process due to bureaucratism, rationalism, myths and ceremonies, isomorphism, and legitimacy whereas institutional logics and agency of social actors support for Paris Climate Agreement and 17 Sustainable Development Goals (SDGs). Hence, the Quintuple Helix Model with Mode 3-Knowledge production is used to redesign universities’ conventional structures. This study perused two sources of data, document analysis, and interviews. Data collected from documents were analyzed by axial coding. After that, interview data from five internal stakeholders were collected based on priori codes, themes, and concepts developed with document analysis. They were thematically analyzed for triangulation. Finally, the theory was developed by induction underpinning with interpretive philosophy when redesigning universities’ conventional structure. The proposed model designed is called “Green University System” to facilitate the production of glocal green knowledge and innovation for sustainable development with Mode 3 and Quintuple Helix model of innovation.