Carbonized polymer dots (CPDs) are attractive optoelectronic materials for a variety of applications, but their complex structures hinder a full understanding of their photophysical and excited-state properties. This work illustrates that heteroatom doping (N-doped, N,S-doped, and N,S,F-doped CPDs) significantly affects the exciton behavior of CPDs. It reveals unconventional photoluminescence (PL) blinking with multilevel intensity fluctuations, which depend on the doping type and excitation power density. The multilevel PL blinking is attributed to the formation of charged excitons induced by heteroatom doping, which resembles the characteristic behavior of semiconductor quantum dots. Additionally, nonradiative recombination enhances photothermal conversion efficiency, enabling effective photothermal therapy with significant cytotoxicity against cancer cells. Our results provide compelling evidence that CPDs possess quantum properties similar to those of semiconductors instead of emissive chromophores on the surface, while also highlighting their multifunctionality as photoluminescent probes and photothermal agents.