Separation of bentonite from wastewater is challenging because bentonite, is highly dispersible in water. Using cationic polymer flocculants has a high flocculation effect on bentonite. However, the flocculation mechanism is unclear. In this study, flocculation, filtration, and bentonite adsorption behavior are investigated using cetyltrimethylammonium bromide (CTAB) as cationic small molecule; subsequently, the flocculation mechanism of bentonite is explored. The flocculation effect increases and the filtration time is reduced with increasing CTAB concentration. In particular, when more than 1500 ppm of CTAB is used, the filtration time is reduced to 2–3 min. Bentonite forms secondary flocculates after the formation of primary flocculates with increasing CTAB concentration. Additionally, the adsorption behavior reveals that CTAB is inserted between the layers, and it is excessively adsorbed on the bentonite surface. The increase CTAB concentration was effective in improving the shortening the filtration time owing to the formation of large bentonite flocculates.