This study aimed at analyzing the level of system governance of the participatory health region and the committee roles on system governance; and categorizing system governance of the participatory health regions at national level. Mixed methods of both quantitative and qualitative studies were used. The study covered 13 health regions. The study population consisted of 638 committee members and secretariat teams. Quantitative data were collected by self-administered questionnaires designed according to United Nations’ good governance criteria, and analyzed by descriptive statistics and exploratory factor analysis. Qualitative data were collected by in-depth interview, focus group discussion, report review and observation, and analyzed by content analysis. The study took 15 months from October 2018 to December 2019. Quantitative analysis showed that the participatory health regions had high system governance level since all components got scores greater than 2.5. The top three highest scores consisted of following the rules of law (score 4.01), equity and inclusive coverage (score 3.91) and transparency (score 3.81). The three least scores included efficiency and effectiveness (score 3.65), accountability to people (score 3.66) and responsiveness to target population (score 3.72). Qualitative data analysis revealed 20 important committee roles on the system governance. Holistic care provision and regular meeting reporting got the same highest levels (score 4.04) while the least achievement role was on fulfilling the setup plans (score 3.48). By factor analysis, two categories of system governance were found: the planning and the implementation process. The present study suggests that the network governance can be used to strengthen both the National Health Security Office’s area health and the regional health of the Ministry of Public Health. Public relations, experience sharing in working with soft power, and building collective leadership are recommended for improving system governance. The weakness of the present study was the lack of impact evaluation.