The analysis of pollution source composition of composite polluted water bodies is currently a challenge in water pollution source identification. The aqueous fluorescence fingerprint technology based on the fluorescence excitation-emission matrix is the key method to solve this problem. This study applied aqueous fluorescence fingerprint technology to perform the pollution source identification analysis of Y River in southern Jiangsu region. The fluorescence signal of textile printing and dyeing wastewater in the Y River derived from allochthonous upstream inputs, which was effectively identified by parallel factor analysis and aqueous fluorescence fingerprint comparison.Heavily contaminated regions were divided by ammonia nitrogen concentration. 109 outlets in the Y River Basin were screened by aqueous fluorescence fingerprint. 35 main responsible units were accurately located through the pollution path tracking method. After implementing the rectification requirements, the water quality of Y River was rapidly improved from below Class Ⅴ to Class Ⅲ and steadily met the standards. The Y River regulation project was cancelled, significantly reducing costs and improving efficiency. In this work, a new model of precise pollution source identification and minimally invasive control was proposed for composite polluted rivers based on aqueous fluorescence fingerprint technology, which is of great significance for realizing pollution control in a precise, science-based, and lawful way.