A novel chemiluminescence (CL) system for determination of permanganate index (CODMn) combined with flow injection analysis has been proposed in this study. On the basis of the chemiluminescent reaction of luminol-KMnO4 system, light emission caused by luminol-KMnO4 system was detected by the photomultiplier tube, and its intensity caused by the appearance of KMnO4 after sample digestion was inversely proportional to CODMn. Effects for CODMn determining such as pH, concentrations and interference were investigated in detail. A detection limit of 0.3 mg/L CODMn with a linear range of 0.3-200 mg/L for its theoretical CODMn was obtained under the optimized experimental conditions. The relative standard deviation was 4.3% for 5.0 mg/L CODMn (n = 11). This CL flow system for determining CODMn was simple, rapid, and suitable for automatic analysis. The data obtained by the present method were fairly in good agreement with those obtained by the standard titrimetric method. It has been applied to determine real samples with satisfactory results.