Carbonized polymer dots (CPDs) have received tremendous attention during the last decade due to their excellent fluorescent properties and catalytic performance. Doping CPDs with transition metal atoms accelerates the local electron flow in CPDs and improves the fluorescent properties and catalytic performance of the CPDs. However, the binding sites and the formation mechanisms of the transition-metal-atom-doped CPDs remain inconclusive. In this work, Mn-ion–doped CPDs (Mn-CPDs) are synthesized by the hydrothermal method. The Mn ions form Mn-O bonds that bridge the sp domains of carbon cores and increases the effective sp domains in the Mn-CPDs, which redshifts the fluorescence emission peak of the Mn-CPDs slightly. The Mn ions form covalent bonds in the CPDs and remedy the oxygen vacancies of the CPDs, which cuts off the non-radiative–recombination process of the Mn-CPDs and increases the quantum yield of the Mn-CPDs to 70%. Furthermore, the Mn-O bonds accelerate the electron flow between adjacent sp domains and enhances the electron transport in the Mn-CPDs. Thus, the Mn-CPDs demonstrate excellent catalytic performance to activate hydrogen peroxide (HO) and produce hydroxyl radicals (•OH) to degrade methylene blue (MB) and rhodamine B (RhB).