The ionic exchange modification mechanism between cationic organic modifier, cetyltrimethylammonium bromide (CTMAB), and two layers of Lou soil, tillage layer (TLLS) and clay layer (CLLS), were studied. The results show that a simple and effective index, sum of amounts of CTMAB and Ca2+/2 (Scc), can be used to judge the essence of modification mechanism between CTMAB and Lou soil. St(CC) demonstrates that the modification of CTMAB to two layers of Lou soil is the coexist of both ionic exchange and hydrophobic bond mechanism. The hydrophobic bond modification appears in the range of modification ratio 20%-28% CEC and linearly increases with an increase of both modification ratio and molar fraction of CTMAB, but its effects on the properties of soil become emergence just until 50% CEC modification ratio, and the hydrophobic bond mode exceeds the ionic exchange mode at about 100% CEC modification ratio and becomes main modification mechanism. The Vanselow selectivity coefficients show that the adsorption preference of Lou soil to CTMAB is stronger than that to calcium ion. The results of thermodynamics indicate that with an increase of modification ratio, the modification reaction transform from exothermic and entropy decrease to endothermic and entropy increase in the range of modification ratio 25% -100% CEC, while both pseudo enthalpy change and pseudo entropy change display a decrease trend in the range of modification ratio 100%-200% CEC, and in total, the modification reaction is a spontaneous reaction which controlled by entropy change in range of modification ratio 25% -100% CEC but controlled by enthalpy change in range of modification ratio 100%-200% CEC. The rationality of modification mechanism could be demonstrated by the results of thermodynamics.