Due to reduce the damaging effect of superstructures subjected to strong earthquakes, isolation technology is widely used in infrastructure construction, such as in hospitals, teaching buildings, and so on. Many significant research achievements have been achieved with respect to base-isolated structures (BISs). Although isolation technology has been maturing over several decades of development, a number of questions remain. The influence on BISs subjected to strong ground motion, and environmental and other loads, the rationality of structure design, and the performance of BISs buildings that have experienced earthquakes must still be verified by structural health monitoring operation. A BIS structural health monitoring system consists of sensory system, data acquisition and transmission system, data processing and control system, structural health data management system, structural health evaluation system, and inspection and maintenance system. Based on site inspections, prior monitoring of dynamic parameters based on BIS characteristics has been proposed. The monitored data should include seismic ground motion, temperature and humidity of the isolation layer, the foundation settlement and wind load (high-rise BISs), horizontal and vertical static displacement of the isolation bearings, vertical strain on the isolation bearings and strain of the isolation layer girder, and horizontal and vertical dynamic displacement of the isolation bearings and acceleration response of the superstructure. Considering the BIS characteristics, in this paper, we propose the primary subjects to be monitored, and consider the general overall design requirements of a BIS health monitoring system. According to different monitoring variables (global and local), we propose basic principles for the sensors selection and layout, and the hardware and software designs of the data acquisition and transmission system. We also present approaches to the design verification and safety performance evaluation. Finally, we address the problems which need to be further studied with respect further study with respect to the influence rule for isolation bearing in the construction process, concrete shrinkage of the superstructure, and setting the site of the post-poured strip; temperature load spectrum and a correlation model of BISs with temperature; how to assess the performance of a BIS while isolation bearing in parallel caused an initial displacement; questions about the fatigue of BISs subjected to earthquakes and wind load; and questions about the rule of progressive and anti-progressive collapses of BISs.