The rheological behavior in a binary system of cetyltrimethylammonium chloride (CTAC) and counter ion salts aqueous solution was studied using MARTINI force field coarse-grained molecular dynamics (CGMD) simulations. The results show that the shear viscosity of the surfactant aqueous solution has a plateau at low shear rates and a shear-thinning regime at high shear rates, which are consistent with the published data. Meanwhile, the shear viscosity increases with increasing the concentration ratio (R) of the counter ion salt to CTAC surfactant, but when R > 1.0, the shear viscosity increases slowly and it appears to reach a plateau. This simulation result agrees with Sureshkumar's report that the mechanical properties of a surfactant-counter ion salt micelle will be stable when CTA+ ions carry the maximum number of Sal− ions (R = 1.0). Then the correlation between the shear viscosity and the micellar structure was analyzed by investigating the micelle morphology and the final largest micelle size under various shear flows. It shows that the network, branched, and wormlike micelles formed by low shear rate, no shear rate, and high shear rate, respectively. The network structure corresponds to the highest shear viscosity and the wormlike resulting in the lowest viscosity. Furthermore, the simulation suggests that increasing temperature and/or shear rate can promote the micelle growth in surfactant aqueous solution. At last, we simulated the effect of counter ion salts on the micelle formation and found that the final largest micelle of CTAC/NamSal binary system is bigger than that of CTAC/NaSal followed by CTAC/NaCl, which agrees with the published experiments.