Residual manganese(II) in finished water undergoes further oxidation and deposition in drinking water distribution systems (DWDS), and Mn deposits can function as sites for accumulating organic and inorganic pollutants. This study aims to explore how Mn transformation and deposition affect the formation of disinfection byproducts (DBPs) in chlorinated DWDS, and trihalomethanes (THMs) was selected as a representative DBP. In a 100 μg/L Mn system, regulated THMs (chlorinated/bromated-THMs) increased by over 20% higher than Mn-free system after 150-day operation; when 50 μg/L iodide (I−) entered pipe systems after 150 days, iodinated THMs (I-THMs) in 100 μg/L Mn system increased by over 30% compared with Mn-free system. These promotions were attributed primarily to the accumulation of biomolecules and organic substances by tight and hard chlorinated Mn deposits. The residence of inactivated cells and the bridging role of surface Mn(III) in Mn deposits increased the quantity of THM precursors in DWDS. Furthermore, the rapid catalytic oxidation of Mn(II) by preformed Mn oxides (MnOx) inhibited the conversion of free iodine (HOI/OI−) to iodate, resulting in the generation of more I-THMs. This study provides new insights into the DBP risks caused by Mn in DWDS.