Drip irrigation technology has obvious advantages in solving the shortage of agricultural water. The demand for using low-quality water sources for irrigation is becoming urgent. Research on the physical blockage formation has become the main part of solving the emitter blockage in China. The purpose of this study is to investigate the blockage characteristics of the emitters in the drip irrigation system with a low-quality water source and to provide some basis for the anti-clogging measures. Therefore, we configured different concentrations (1.8 g/L, 2.8 g/L, 3.8 g/L) and different particle sizes (0–0.054 mm, 0.054–0.075 mm, 0.075–0.1 mm) of low-quality water sources and carried out drip irrigation tests. The holistic and local characteristics of the physical blockage occurrence and distribution were compared under the sand-laden water source irrigation, then the structure and element composition of the blockage material were analyzed. The results show that the clogging characteristics are related to the emitter types, sediment content, and sediment particle size. The higher sediment concentration means that the single emitter is more likely to be blocked completely, and the whole clogging development is short and quick. However, at lower sediment concentration treatments, the probability of complete clogging decreases, and the clogging process is uniform and slow. The blockage position of large flow channel emitters (E1) appears at the head and middle of the drip irrigation tape, and the internal blockage usually occurs at the inlet. The small size channel emitters (E2 and E3) are concentrated in the head and end of drip irrigation tape, and the internal blockage usually occurs in the low-speed zone of the labyrinth channel such as the inlet fence. The internal blocked material is the accumulation structure formed by sediment particles and the coupled precipitation aggregate formed by the reaction of various chemical ions. Among them, the mixing of large and small sediment particles is more inclined to form a stable blocking skeleton structure.