Drip irrigation using reclaimed water or polluted surface water involves a higher risk of bio-clogging, which is the most typical and the most complex type of clogging, and the clogging of drip irrigation emitters limits the use and spread of drip irrigation technology. Due to its strong oxidizing effect, chlorination has been considered as the most effective method of controlling emitter bio-clogging. However, the detailed controlling mechanism has remained unclear until now. Meanwhile, there have been no unified standards established for chlorination to refer to. Therefore, field experiments were carried out in a sewage treatment plant, where the reclaimed water after secondary treatment was treated with the Cyclic Activated Sludge System (CASS) process that had been incorporated to the drip irrigation system to study the controlling mechanism and impacts on non-pressure-compensating emitter bio-clogging. There were three chlorination treatments studied, which included 2.5mg/L×2h (low concentration, long duration), 5.0mg/L×1h (moderate concentration and duration), and 10mg/L×0.5h (high concentration, short duration). The results showed that the chemical chlorination could control the microbial growth in the bio-clogging substances effectively, with the microbial phospholipid fatty acids (PLFAs) decreased by 8.3%–36.1%, the number of microbial species decreased by 2–3, the microbial activity decreased by 2.6%–23.2%, and the secretion of extracellular polymeric substances (EPS) decreased by 19.8%–43.4%. Thus, the bio-clogging substances were well controlled, and the contents of solid particles (SD) content decreased by 4.8%–48.2% compared to the non- chlorinated treatment, while the discharge ratio variation (Dra) and Christiansen uniformity coefficient (CU) increased by 14.7%–22.8% and 6.77%–19.9%, respectively. However, the effects of different chlorination modes varied significantly. Chlorination with a low concentration and a long contacting duration decreased microbial activity, and better controlled emitter bio-clogging. Thus, the chlorination treatment of 2.5mg/L×2h was recommended in the drip irrigation system using reclaimed water treated with CASS technology.