The health information system is a component of the healthcare system. The health information system in health services in Indonesia has experienced many problems in getting support for policy making, the implementation of the industrial revolution 4.0, and national health insurance (JKN). To answer the above problems, it is necessary to make a concept of health information systems in health services that based on environment and one health perspectives. This research was part of the thematic research of the 2019 JKN National Health Facilities Survey (Rifaskes) in Indonesia. The systems approach and cross-sectional research were carried out by collecting quantitative data. A structural equation model with Lisrel 88 software was used to model the health information system. The health information system produced a concept that included the following structured input components: governance, human resources, infrastructure, types of information system (IS) (program, JKN, management), and financing; process components: funding, technical guidance, and verification and validation; and output components: open access, standards and quality, utilization, bridging, and security. The concept for strengthening the health information system prioritizes improving the output components (standards, utilization, bridging, open access, and security) in the process components (funding, verification, technical guidance) while the input components (financing, human resources, governance, IS programs, infrastructure, IS JKN, IS management).