Mixing Yellow River water with brackish water for drip irrigation can be an effective solution of water shortage because the mixed water contains less sediment and salinity. However, the mixed water can still cause emitter clog and significantly reduce drip irrigation system performance because of the sediment particles and salt separators. The surface morphology of the clogging substance is an integral reflection of multiple factors. Therefore, three different types of water, including the Yellow River water (YR), brackish water (SW) and mixed water (MW) of Yellow River water and brackish water at the mixing ratio of 1∶1 were used to cultivate the emitter’s clogging substance. The effect of the mixed water on the surface characteristics was studied by 3D white-light interference profilometer. The results showed that the surface of clogging substance in condition of the mixed water was less protruding and more flat, the thickness, Sq and Sdr were decreased significantly. At the end of the system operation (800h), the average thickness of the clogging substance under the mixed water was 4.39μm, which was 65.32% and 32.51% lower than that of the Yellow River water and brackish water, respectively. The result showed that the mixed water can not only effectively reduce the sediment content in the Yellow River water, but also reduce the salt content in the brackish water. The mixed water relieved emitter’s clogging effectively because of low sediment content and salinity.