The source and temporal changes of minerals transported by the world’s large rivers are important. In particular, clay minerals are important in evaluating the maturity of suspended sediments, weathering intensity, and source area. To examine seasonal changes in mineralogical compositions of the Changjiang River (CR), suspended particulate matter (SPM) samples were collected monthly for two hydrological cycles in Nanjing city and then were studied using X-ray diffraction (XRD), diffuse reflectance spectrophotometry (DRS), X-ray fluorescence spectrometry (XRF), and chemical analyses. The results indicate that the concentration of CR SPM ranges from 11.3 to 152 mg/L and is highly correlated to the rate of water discharge, with a greater concentration in flood season and lower concentrations during the dry season. CaO, MgO, and Na2O increase with increasing discharge whereas Al2O3 decreases sharply with increasing discharge. Dolomite, calcite, and plagioclase show strikingly similar seasonal variations and increase with increasing discharge with maximum concentrations in the flood season. In contrast, the clay mineral content exhibits the opposite trend with the lowest concentrations in the flood season. Illite dominates the clay minerals of the CR SPM, followed by chlorite, kaolinite, and smectite. Illite and kaolinite show distinctly seasonal variations; SPM contains more illite and less kaolinite during the flood season than during the dry season. The illite chemistry index and crystallinity, as well as kaolinite/illite ratio, all indicate intense physical erosion in the CR basin during the rainy season. Total iron (FeT) and highly reactive iron (FeHR) concentrations display slight seasonal changes with the smallest values observed during the flood season. Goethite is the dominant Fe oxide mineral phase in the CR SPM and hematite is a minor component, as revealed by DRS analyses. The FeT flux and FeHR flux are 2.78×106 T/y and 1.19×106 T/y, respectively.