The high speed of contaminants growth needs the burgeoning of new analytical techniques to keep up with the continuous demand for monitoring and legislation on food safety and environmental pollution control. Metal-organic frameworks (MOFs) are a kind of advanced crystal porous materials with controllable apertures, which are self-assembled by organic ligands and inorganic metal nodes. They have the merits of large specific surface areas, high porosity and the diversity of structures and functions. Latterly, the utilization of metal-organic frameworks has attracted much attention in environmental protection and the food industry. MOFs have exhibited great value as sensing materials for many targets. Among many sensing methods, fluorometric sensing is one of the widely studied methods in the detection of harmful substances in food and environmental samples. Fluorometric detection based on MOFs and its functional materials is currently one of the most key research subjects in the food and environmental fields. It has gradually become a hot research direction to construct the highly sensitive rapid sensors to detect harmful substances in the food matrix based on metal-organic frameworks. In this paper, we introduced the synthesis and detection application characteristics (absorption, fluorescence, etc.) of metal-organic frameworks. We summarized their applications in the MOFs-based fluorometric detection of harmful substances in food and water over the past few years. The harmful substances mainly include heavy metals, organic pollutants and other small molecules, etc. On this basis, the future development and possible application of the MOFs have prospected in this review paper.