Development of innovation that affected by information systems such as BPR (Business Process Reengineering) and ERP (Enterprise Resource Planning) are becoming a trend in recent decades to achieve performance improvement. To be able to formulate a strategy of higher education innovation that is part of strategic management, research needs to be done on the model of organizational innovation, information systems, and strategic innovation. This research used expert judgment and SEM (Structural Equation Modeling) to obtain the variables of designated model. The factors that affect the most to organizational innovation performance is Organizational Change with a total effect of 0.619 for Jakarta, 0.679 for Bandung, and 0.679 for Bogor. Specifically, the most affecting is coordination improvement. This research shows that in higher education, organizational innovation depends more on the process.