Disease diagnostics, food safety monitoring and environmental quality monitoring are the key means to safeguard human health. However, conventional detection devices for health care are costly, bulky and complex, restricting their applications in resource-limited areas of the world. With the rapid development of biosensors and the popularization of smartphones, smartphone-based sensing systems have emerged as novel detection devices that combine the sensitivity of biosensors and diverse functions of smartphones to provide a rapid, low-cost and convenient detection method. In these systems, a smartphone is used as a microscope to observe and count cells, as a camera to record fluorescence images, as an analytical platform to analyze experimental data, and as an effective tool to connect detection devices and online doctors. These systems are widely used for cell analysis, biochemical analysis, immunoassays, and molecular diagnosis, which are applied in the fields of disease diagnostics, food safety monitoring and environmental quality monitoring. Therefore, we discuss four types of smartphone-based sensing systems in this review paper, specifically in terms of the structure, performance and efficiency of these systems. Finally, we give some suggestions for improvement and future prospective trends.