Booster chlorination was usually employed in water distribution systems with a long hydraulic retention time. The free chlorine decay and disinfection by-products (DBPs) transformation under booster chlorination conditions were investigated within a pilot-scale water distribution system (WDS). Compared with the initial chlorination in water plants, the loss of chlorine was relatively slow and could be described with first-order kinetic model. The rate of chlorine decay and the generation of DBPs in WDS were much greater than those in beaker. High flow rate and the hydraulic transients both promoted chlorine decay and DBPs formation, especially for dichloroacetonitrile (DCAN). The formation of trihalomethanes (THMs) and haloacetic acids (HAAs) was higher in the ductile iron pipe than in the steel pipe. After booster chlorination, THMs, HAAs, and DCAN all climbed up and then declined continuously, but the peak times were different during the reaction process. The results showed the generation period of DBPs followed the order: THMs (27 h) > HAAs (22 h) > DCAN (5 h). DCAN was not stable in WDS and could be decomposed for a long hydraulic retention time (HRT). The decrease of dichloroacetic acid (DCAA) and increase of trichloroacetic acid (TCAA) indicated that DCAA may turn into TCAA. Linear relationships between the free chlorine demand (FCD) and the generation of THMs that considered both buck water and the pipe wall, as well as the different hydraulic conditions, were established to predict the formation of DBPs in WDS after booster chlorination.