Mechanical control of magnetism is an important and promising approach in spintronics. To date, strain control has mostly been demonstrated in ferromagnetic structures by exploiting a change in magnetocrystalline anisotropy. It would be desirable to achieve large strain effects on magnetic nanostructures. Here, using in situ Lorentz transmission electron microscopy, we demonstrate that anisotropic strain as small as 0.3% in a chiral magnet of FeGe induces very large deformations in magnetic skyrmions^,, as well as distortions of the skyrmion crystal lattice on the order of 20%. Skyrmions are stabilized by the Dzyaloshinskii–Moriya interaction^,, originating from a chiral crystal structure. Our results show that the change in the modulation of the strength of this interaction is amplified by two orders of magnitude with respect to changes in the crystal lattice due to an applied strain. Our findings may provide a mechanism to achieve strain control of topological magnetic structures based on the Dzyaloshinskii–Moriya interaction.