Fluorescent probes are widely used in biomedicine, information storage, chemical analysis and other fields due to their high sensitivity, real-time detection, accurate diagnosis and imaging visualization. Among them, borondipyrromethene (BODIPY)-based fluorescent probes are widely designed and developed because of their excellent photophysical and chemical properties. In this review, the molecular design strategies and functional applications of formyl substituted BODIPY fluorophores were summarized and discussed, including α/β-formyl substituted BODIPYs, meso-formyl BODIPYs and 1,7-formyl BODIPYs with different positions, and their applications in anions detections, biological thiol recognition and biological imaging. Design of new formyl substituted BODIPY-based probes shows great development potential in precise diagnosis and treatment in the future.