Environmental pollution, food safety and health are closely linked. A key challenge in addressing the problem of food safety and protecting public health is building an integrated knowledge base to inform policy and strengthen governance. This requires breaking down the trans-departmental information barrier across the environment, food and health domains to ensure the effective flow of data and the efficient utilization of resources, and facilitate the collaborative governance of food safety. Achieving this will be crucial for the development of health and medical care in China in the era of big data. Currently, the information resources commanded by various departments are incomplete and fragmented. Data resources are also organized in vertical silos and there is a lack of data sharing within and across policy streams. To provide the basis for more effective integrated collection and analysis of data in future, this study summarizes the information resources of various departments whose work relates to interactions between environment, food and health, and presents measures to strengthen top-down design, and establish unified data standards and a big data sharing platform. It also points to the need for increased training of data analysts with interdisciplinary expertise.