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This paper presents a methodology to prioritize suitable criteria and their sub-criteria for science education through flipped e-learning programs. Here, an operational technique is applied together with multi-criteria decision analysis (MCDA) and fuzzy-decision-making trial and evaluation laboratory (F-DEMATEL) method to outline different components such as instructors, courses and laboratories, materials, technological infrastructures, securities, etc. in flipped science education. In the context of MCDA/F-DEMATEL hybrid and participatory approach, we have selected three major criteria after experts- consultation through analytic hierarchy process (AHP), that is, flipped-learning, science-education and technological-advance. Their weight coefficients and influence are calculated to rank their suitability in a more long-term learning program. With the weighted linear combination (WLC) and sensitivity analysis, the most suitable criteria and sub-criteria are selected for science education through flipped e-learning programs, i.e. technological-advance and infrastructure of information technology. Hence, these operational methods have possibility to be reused and reapplied in different studies and parallel education settings if there are available data. Thus, because online-learning methods are accelerating its development into various learning domains, it could resolve decision-making problems on flipped science education.