Infiltration irrigation with saline water is a more effective method than drip irrigation to alleviate water scarcity worldwide, but so far, no report has discussed the clogging rules of ceramic emitters, a major component of infiltration irrigation system. To explore the clogging mechanism of ceramic emitter in saline water infiltration irrigation system, we used four kinds of saline water sources with electrical conductivity (EC) of 0.18, 1.74, 3.78, and 7.74 ds/m, respectively. In addition, we specifically investigated the law of discharge ratio variation (Dra) of ceramic emitters, as well as the composition and growth process of clogging substance. The results indicated that the Dra of ceramic emitters decreased in the process of saline water irrigation, and the higher the EC, the more obvious the decrease. The calcium carbonate (CaCO3) was the main component of the clogging substance in the inner wall of ceramic emitters. The clogging part was a layer on the inner wall of the emitters rather than the pores in the walls, and the clogging did not occur suddenly. Instead, it was caused by the long–term accumulation of the clogging substance. Moreover, with the increase of EC, the flocculation between the clogging particles in the water was enhanced and thus promoted the formation of stable and compact aggregates, which fundamentally led to the clogging acceleration of ceramic emitters. This clogging mechanism of ceramic emitters can provide some theoretical reference for the establishment of anti-clogging strategy.