Utilizing reclaimed water by drip irrigation technology proves to be an effective strategy for mitigating agricultural water scarcity. Nevertheless, the formation of clogging substances within emitter flow channels poses a significant impediment to the advancement of this technology. Currently, there is a limited understanding of the mechanisms governing the formation of clogging substances in emitter flow channels, primarily due to their semi-closed and narrow characteristics. This study employed industrial computed tomography to delineate the spatial distribution of clogging substances in emitter flow channels and elucidate critical regions prone to substance accumulation. The findings revealed that clogging substances were predominantly situated on the top and substrate faces of the emitter flow channels, comprising 35.7-50.0% and 36.9-44.4% of the total, respectively. In contrast, distribution on the upstream, downstream, and root faces was minimal, each contributing less than 25% to the total. Moreover, there was a notable accumulation of clogging substances at the front of the flow channel, displaying a significant decrease towards the flow direction. The average volume fractions of clogging substances in the front, middle, and back of the flow channel were 7.5-22.8%, 9.0-20.2%, and 6.5-18.7%, respectively. To mitigate emitter clogging, it is recommended to focus on controlling clogging substances on the top and substrate faces, and at the front of the emitter flow channel. In conclusion, this study provides valuable insights into the spatial distribution of emitter clogging substances, paving the way for the development of anti-clogging emitters and the promotion of reclaimed water irrigation technology.