Using sludge obtained from municipal sewage treatment plants, the response of viable bacterial populations during the sludge ozonation process was investigated by a combination of adenosine triphosphate (ATP) assay and propidium monoazide (PMA)-Miseq sequencing. The ATP assay was first optimized for application on sludge samples by adjusting the sludge solid contents and reaction time. PMA-modified polymerase chain reaction (PCR) was also optimized by choosing the suitable final PMA concentration. The quantity and composition of viable bacterial populations during sludge ozonation were further elucidated using the optimized ATP and PMA-modified PCR methods. The results indicated that after the sludge was exposed to ozone (O3) at 135 mg·O3/g total suspended solids (TSS), the viable biomass displayed a substantial decrease, with a reduction rate reaching 70.89%. The composition of viable bacterial communities showed a faster succession, showing that an ozone dosage of 114 mg·O3/g TSS is enough to significantly change the viable bacterial population structure. Floc-forming genera, such as Zoogloea, Ferruginibacter, Thauera and Turneriella, are sensitive to ozonation, while the relative abundances of some functional bacterial genera, including SM1A02, Nitrospira and Candidatus Accumulibacter, remained constant or increased in the viable bacterial population during sludge ozonation, indicating that they are more resistant to ozonation.