Utilizing the anti-Zeno effect, we demonstrate that the resonances of ultracold molecular interactions can be selectively controlled by modulating the energy levels of molecules with a dynamic magnetic field. We show numerically that the inelastic scattering cross section of the selected isotopic molecules in the mixed isotopic molecular gas can be boosted for 2–3 orders of magnitude by modulation of Zeeman splittings. The mechanism of the resonant anti-Zeno effect in the ultracold scattering is based on matching the spectral modulation function of the magnetic field with the Floquet-engineered resonance of the molecular collision. The resulting insight provides a recipe to implement resonant anti-Zeno effect in control of molecular interactions, such as the selection of reaction channels between molecules involving shape and Feshbach resonances, and external field-assisted separation of isotopes.