Fluorescent probes have wide applications in biological and environmental analysis due to their advantages of simple operation, convenient flexibility, high sensitivity and efficiency. They are considered to be promising tools for accurate analysis of agriculture- and food-related hazardous substances. In this review, the types and characteristics of the near-infrared fluorescence probes (NIFPs) are briefly described. The recent advances of NIFPs for precisely detecting various hazardous substances including heavy metals, sulfite and related sulfiting agents and hydrogen peroxide are summarized. Finally, the present challenges and future perspectives faced by NIFPs in food safety analysis are discussed.