To clarify the influence of particle size on the distribution of lateral pipes and clogging of emitter in drip irrigation system, the experiments of short term muddy water and clogging were conducted with eight types of different particle size to investigate the distribution of sediment in different lateral pipes and emitter clogging situation. The results showed that the coefficient of siltation distribution of lateral pipes could be used to measure the nonuniform siltation distribution of sediment in different lateral pipes. The moving state of sediment in branch pipe greatly influenced the amount of sediment entered from lateral pipes. Therefore, the situation of sediment deposited in different lateral pipes could be determined by the suspension index of sediment in branch pipe. The siltation amount was more nonuniform in each lateral pipe when the suspension index was higher. The mutation happened where suspension index was 0.325. In addition, the large particles of sediment moved as the form of bed load at the bottom of lateral pipes, which directly resulted in the unexpected clogging of emitter, and mainly appeared in the first and second lateral pipe. While the flocculation of the fine particles was the main reason causing the clogging of the emitter. The research on the distribution of sediment in lateral pipes and the clogging rule of emitter in drip irrigation system was helpful to deeply understand sediment motion rule in pipe network and provided some references for searching clogging reason of emitters and reasonable arrangement of lateral pipes.