The latest experimental advances have extended the scenario of coupling mechanical degrees of freedom in chiral magnets (MnSi/MnGe) to the topologically nontrivial skyrmion crystal and even monopole lattices. Equipped with a spin-wave theory highlighting the topological features, we devise an interacting model for acoustic phonons and magnons to explain the experimental findings in a monopole lattice with a topological phase transition, i.e., annihilation of monopole-antimonopole pairs. We reproduce the anisotropic magnetoelastic modulations of elastic moduli: drastic ultrasonic softening around the phase transition and a multi-peak-and-trench fine structure for sound waves parallel and orthogonal to the magnetic field, respectively. Comparison with experiments indicates that the magnetoelastic coupling induced by Dzyaloshinskii-Moriya interaction is comparable to that induced by the exchange interaction. Other possibilities such as elastic hardening are also predicted. The study implies that the monopole defects and their motion in MnGe play a crucial role.