This study investigated the effects of heavy metals—lead (Pb), cadmium (Cd), and chromium (Cr)—and the influence of titanium dioxide (TiO2) and silica (SiO2) nanoparticles on the in vitro growth and development of Chrysanthemum morifolium microshoots cultured on Murashige and Skoog (MS) medium. Microshoots were cultured for five weeks on MS medium supplemented with varying concentrations of Pb, Cd, or Cr, individually and in combination with TiO2 or SiO2 nanoparticles. The results demonstrated that supplementation with Pb, Cd, or Cr significantly influenced shoot proliferation, shoot length, leaf number, and biomass accumulation. The addition of TiO2 and Si nanoparticles further enhanced shoot formation and leaf number compared to control treatments. For Pb treatments, the highest number of shoots (14.2 ± 1.29 per explant) was obtained on MS medium containing 1.0 mg/L Pb and 25 mg/L Ti. In the presence of Cd, shoot multiplication increased notably, with the maximum number of shoots (15.84 ± 1.93) achieved at 6.0 mg/L Cd and 25 mg/L Si nanoparticles. Similarly, Cr treatments enhanced shoot regeneration, with the highest number of shoots (15.6 ± 1.02) observed at 6.0 mg/L Cr and 25 mg/L Si. Although shoot length generally decreased with increasing heavy metal concentrations, the number of leaves and both fresh and dry biomass increased significantly (p < 0.05) in the presence of nanoparticles. Metal uptake analysis revealed that Pb and Cd accumulated in the explants proportionally to their concentrations in the medium, while Cr absorption remained negligible. Overall, moderate levels of Pb, Cd, or Cr, particularly when combined with TiO2 or Si nanoparticles, promoted in vitro morphogenesis and biomass production in C. morifolium. However, concentrations beyond optimal levels exhibited inhibitory effects on growth parameters.