Permanganate index (COD_Mn) is an important parameter for water quality assessment and pollution control supervision in China. Its concentration reflects the severity of organic pollution. Since the Three Gorges Reservoir was put into operation in 2003, the hydrological condition of in the middle and lower Yangtze River mainstem has been changed significantly. Therefore, the characteristics of spatiotemporal distributions of organic substances(OS) corresponding to permanganate index in the middle and lower mainstem of the Yangtze River under new hydrological condition were studied. The results show that in the middle and lower reaches of the Yangtze River: Since 2004, COD_Mn has been decreasing generally, and it is currently at a low level and tends to stabilize. The trend of COD_Mn in the different river sections and the water period is inconsistent. OS(COD_Mn) in the water column are mainly in the dissolved state, and the proportion of the dissolved state tends to decrease along the direction from upstream to downstream. The median values of C_clarified/C_original ratio in Nanjinguan, Hankou and 23 km below Wusongkou, are 0.862, 0.734 and 0.598 respectively. The effect of the precipitable particles on the COD_Mn concentration in the water is low, especially in the upstream section. The median values of (1-C_filtered/C_original) ratios in Nanjinguan, Hankou and 23 km below Wusongkou were 0.138, 0.266 and 0.402, respectively. There is no significant difference between the different lines and measuring points in the transverse profile in the section on upstream end of studied reach, but significant difference in the estuary section, especially between the surface layer and the bottom layer in the vertical direction. Oxygen-consumed organic pollution is not serious in the coastal waters of urban reaches, and the average concentration of COD_Mn of the clarified samples is between 1.91 and 3.45 mg/L, and the concentration value is seldom higher than 6.0 mg/L.