Kidney-related diseases such as acute kidney injury, chronic kidney disease, and kidney tumors pose a serious threat to human health. Early diagnosis and dynamic monitoring of these diseases are of great significance for revealing pathological mechanisms, evaluating the degree of injury, and improving patient prognosis. Near-infrared fluorescence imaging has shown broad application prospects in the research and diagnosis of kidney diseases due to its advantages, including deep tissue penetration, low spontaneous fluorescence interference, high sensitivity, and suitability for real-time in vivo imaging. This article first outlines the key pathological processes and important biomarkers involved in the occurrence and development of kidney diseases. Then, a classification review is conducted around reactive oxygen species, reactive nitrogen, reactive sulfur, enzymes, and microenvironment-responsive near-infrared fluorescent probes. Combined with their representative applications in acute kidney injury, chronic kidney disease, kidney tumors, and urine sample analysis, the design strategies, imaging performance, and diagnostic and therapeutic potential of relevant probes are summarized. Finally, this article discusses the main challenges faced in this field from the aspects of detection specificity, quantitative accuracy, deep imaging capability, biosafety, and clinical translational feasibility, and looks forward to future development directions.