In this paper, for multipath parameter estimation of SC-FDE systems, two classic methods, one is time domain estimation and the other is frequency domain estimation, are briefly introduced firstly. Then theoretical analysis and comparison between above two methods are presented, including advantages and disadvantages, estimated accuracy, and implementation complexity. On this basis, the multipath parameter estimation using two methods are simulated and simulation results are analyzed comparatively. Then it is concluded that the two methods have the same MSE and BER performance.