Emitter clogging is one of the bottlenecks that restricts the application and promotion of drip irrigation technology. Applying intermittent fluctuated water pressure is regarded as an effective way to overcome drip irrigation emitter clogging when using high sediment water. Therefore, a drip irrigation experiment using Yellow River water was carried out at Deng Kou County, Inner Mongolia, China, to study emitter clogging controlling effects of three fluctuation patterns. The control group (CG) operation pressure was 40 kPa, and three intermittent fluctuated water pressure modes were 40 kPa + fluctuating water pressure for 1 h (FP1 h), 2 h (FP2 h), and 4 h (FP4 h), respectively. The system was fluctuated once every 16 h, and the amplitude of the fluctuating water pressure was 80–100 kPa with a cycle of 40 s. The characteristics of the sediment size and mineral components of clogging substances found in emitters and laterals were also analyzed. The results showed that intermittent fluctuated water pressure not only directly changed the flow velocity distribution in the emitter flow path to reduce the deposition of clogging substances, but also controlled the formation of clogging substances inside the laterals to avoid enhanced emitter clogging by transporting into the emitter. The intermittent fluctuated operating pressure could effectively reduce contents of emitter clogging substance in drip irrigation, and the longer period it was applied, the better controlling effect was observed. Comparing with the CG, applying intermittent fluctuated water pressure with constant period of 4 h would reduce the total clogging substance contents by 26%. The clay and powder particles were reduced by 56% and 34%, respectively. Meanwhile the quartz, silicate, calcium magnesium and carbonate in the clogging substances decreased by 36%, 35%, and 11%, respectively. Thus, the discharge ratio variation coefficient (Dra) and Christiansen Uniformity coefficient (CU) increased by 10.1–16.7% and 8.9–14.2%, correspondingly. These results could provide references for the application and promotion of drip irrigation technology using water with high sediment load.