The six typical different parts of soils and sediments along the bank of the Three Gorges Reservoir Area (TGRA) were collected, and the humic substance isolated from the six parts of the soils and sediments’ samples was separated to humic acid and fulvic acid, purified, and characterized with the combination of the Raman and IR vibrational spectroscopic technologies after cool-dried separation; through assigning the vibrational peaks in each part of the Raman and IR spectra of each sample part, the vibrational characteristics of the structures and the groups that belonged to the molecules of the humic acids and the fulvic acids in the soils and sediments of the TGRA were obtained; the changing features of the groups and structures in the humic acid and the fulvic aicd’s molecules from the different soils and sediments in the TGRA were discussed with the environmental impact factors such as soil humic degree, the conditions of different soils conference, using and/or cultivating models and water level fluctuations. From the experimental results, the vibrations about C—O, C—C, and poly-hydrogen bonds dominate in the structures and the groups of each part’ humic substance; the active vibration numbers in the upstream are more than in the downstream; the soil’s humic degree has great effect on the formation of the humic substances’ structures in soil’s humic substance; the soil used as agricultural cultivating mode showed higher humic degrees in the upstream parts of the TGRA. The effect of the water level’s fluctuation on the formation of the humic acid and fulvic aicd in the sediments of the TGRA is not obvious in the short time.