Overwhelming evidence suggests that nanozymes show great promise in cancer therapy due to their stable catalytic properties and cost-effectiveness. However, the diverse responses of nanozymes in therapy have presented challenges. After designing pH-sensitive Fe3O4/MnO2@DOX hybrid nanozymes with catalytic properties, we analyzed their characteristics using various techniques such as SEM, TEM, DLS, XRD, TGA, EDS, etc. We evaluated the nanozymes' toxicity on MCF-7 cells and their spheroids through MTT and flow cytometry assays, while also exploring their synergistic effects with photothermal therapy (PTT). The findings reveal that the 150–270 nm Fe3O4/MnO2@DOX hybrid nanozymes demonstrate stable DOX release and catalytic activity in generating O2 and °OH, effectively inhibiting the growth of MCF-7 cells. It was found that the effective concentration for MCF-7 cells had to be raised from 2.13 to 4.64 µg/mL to inhibit spheroid growth. Because of the toxicity of this concentration on normal cells, using synergistic approaches is crucial to minimize side effects. Also, the results of cytotoxicity mechanism in spheroids highlight the significant impact of PTT with Fe3O4/MnO2@DOX hybrid nanozymes in enhancing pro-inflammatory cytokines like TNF-α, CASP9, CASP7, and CASP3. Ultimately, optimizing the concentration of pH-sensitive hybrid nanozymes with PTT synergistic effects shows great potential for cancer treatment.