Bisphenol A (BPA) is an important emerging contaminant with endocrine-disrupting potential that has frequently been detected in aquatic environments. In this study, two types of hierarchically structured manganese dioxide/biochar nanocomposites (MnO₂/BCs) were prepared for the first time via facile hydrothermal synthesis. The hydrothermal reaction was maintained at 100 °C for 6 h or 12 h, after which an ultrasound-assisted heterogeneous Fenton-like process was used to catalyze the removal of BPA under neutral pH condition. The characterization results indicated that MnO₂ nanoparticles were successfully formed on the nanocomposite surfaces and had flower-like (δ-MnO₂, 6 h) and urchin-like (α-MnO₂, 12 h) morphology. This enabled a significant improvement in the catalytic activity of BPA removal by the reversible redox reaction. A series of experiments confirmed that the crystalline properties of the nanocomposites affected their catalytic activity. In particular, the α-MnO₂/BCs exhibited catalytic activity in the ultrasound-assisted heterogeneous Fenton-like process and completely removed BPA within 20 min under the following conditions: [BPA]₀ = 100 μM; [H₂O₂]₀ = 10 mM; [catalyst]₀ = 0.5 g/L; ultrasound = 20 kHz (130 W) at 40% amplitude; pH = 7.0 ± 0.1; and temperature = 25 ± 1 °C. This efficiency may have been due to the synergistic effect of ultrasound and α-MnO₂/BCs, which simultaneously induce the effective generation of reactive free radicals and increase the mass transfer rate at the solid-liquid interface. Overall, these results demonstrated that hierarchical urchin-like α-MnO₂/BCs have significant potential as an efficient and low-cost catalyst in ultrasound-assisted heterogeneous Fenton-like systems.