This paper investigates the effects of pilot choice for the channel estimation of the single carrier cyclic prefix-assisted CDMA system. The optimal pilot problem for die least square channel estimation is formed as a discrete optimization problem. Because the computation to Find the optimal solution is too huge the heuristic method is applied to get several sub-optimal pilots. Different equalization methods are also applied to test the channel estimation performance. The simulation results demonstrate that even the sub-optimal pilots can give more accurate estimation of the channel and improve the system performance considerably.