This study aimed to design and operate a complementary integrated health management program based on the connection between the hypertension and diabetes management programs and the oral health programs at a public health center. It also proposed to suggest the phased evaluation indicators. In this study, 48 adults registered in the hypertension and diabetes management program were selected from the Gangneung public health center. The clinic-specific programs were led by dental hygienists and operated for visitors twice every two weeks. The programs were designed based on the logical model, and indicators for evaluating the structure, process, and outcome were presented and applied to the input, process, output, and outcome. The evaluation indices consisted of quantitative and qualitative indicators, and the planning and operation, goal achievement, and effect of each program were assessed. The process evaluations were assessed by the appropriateness of the managers and the operating fidelity of the programs. Indicators for evaluating the outcomes were gingival bleeding, oral health knowledge, oral health awareness, and the satisfaction of the participant and the manager. The clinic-specific programs resulted in positive changes in the evaluated outcomes. The integrated health management of visitors to the hypertension and diabetes management program is important as the general and oral health has common risk factors. Furthermore, long-term operation and continuous monitoring of oral health programs are necessary to evaluate the common factors in chronic disease management.