The purpose of this study was to apply multicriteria decision making and an analytic hierarchy process (AHP) model for assessing sustainable management of hypertension and diabetes. Perception of two alternative health care priorities was also investigated. One priority was improving treatment compliance of patients with hypertension and diabetes. The other priority was strengthening the healthcare system for continuous care. Our study design to evaluate community-based intervention programs for hypertension and diabetes was developed using brainstorming, Delphi techniques, and content analysis along with literature review. We finally proposed a hierarchical structure of the AHP model with 50 third sub-criteria in six levels. By surveying this AHP questionnaire to a total of 185 community health practitioners in Korea, we found that improving treatment compliance of patients with chronic diseases should be relatively more important than strengthening the healthcare system. Further research is needed to expand survey subjects to primary care physicians and even policymakers of central government for the appropriate application of this AHP model.