Abstract: Sediment deposition has posed a serious risk to the performance of emitter flow channels. This study aims to explore the influences of the emitter performance on sediment deposition, in order to reduce the risk of physical blockage occurrence. Different concentrations (1.8, 2.8, and 3.8 g/L) and particle sizes (0 ≤ d ＜ 0.054 mm, 0.054 mm ≤ d ＜ 0.075 mm, 0.075 mm ≤ d ＜ 0.1 mm) of sandy water were used in the emitter clogging test of intermittent drip irrigation. A comparison was also made on the particle size composition in the sediment output from the emitters that irrigated with the sandy water. A systematic analysis was then implemented for the sediment transport and siltation inside the emitters. A numerical simulation was also carried out to analyze the flow pattern in the emitter. The low-velocity or vortex zone was prone to clogging. An operation mode was finally recommended to improve the clogging-resistant performance of the emitters in the drip irrigation system, according to the flow pattern and the deposited sediments. The results show that: 1) There was a consistent effect of side-seam labyrinth emitters on the size of settled sediment, with a decrease in the specific gravity of clay and sand particles, and the increasing specific gravity of powder particles. The grain size composition of the input original sediment was compared with the output one. There was a decreased proportion of clay and sand particles with an increased proportion of silt particles. Since the water-following property of sand particles was weaker than that of clay particles and silt particles, there was a weak discharge from the emitter with water. Specifically, the proportions of clay particles and sand particles in the sediment decreased by 1.14-2.98 percentage points and 1.55-11.14 percentage points, respectively, whereas, the proportion of silt particles increased by 1.25-13.74 percentage points. 2) The low transport of large particle size was attributed to the small size of the labyrinth emitter flow channel. The clogging of the particle size was concentrated in the range of 0.054-0.1 mm particle size. Most sediment sizes were between 0.002 and 0.05 mm in the flow channel of the emitter, due to the agglomeration of sediment flocs. 3) Streamline in the mainstream area was moving forward in a wave-like manner. The flow velocity in the mainstream area was greater than that in the near-wall area, while the flow velocity at the central corner was large, and a vortex was generated in the upper and lower corners. The inner and outer water bodies in the centrifugal force and water pressure under the joint action of the inner water body flew to the lower wall of the lower runner unit, while the outer water body flew to the upper side wall of the upper runner unit, where the turbulence of the water flow diffusion rate was faster. A vortex area was formed in the inner and outer boundaries of the circulation in the labyrinth runner. Part of the particles was retained in the vortex area, thus causing the runner blockage. That was the main factor for the emitter clogging. After that, sand particles were very easy to settle and concentrate in the vortex center and the water surface. Some suggestions were proposed to reduce the number of right- and sharp-angled areas, in order to reduce the formation of low-velocity zones in the design optimization. The clogging of emitters can be prevented by the sand deposition. The long and narrow over-flow structures can also be avoided, according to the location of the clogging of sediments.