Dynamics of string-like objects is an important issue in a broad range of physical systems, including vortex lines in superconductors, viscoelastic polymers, and superstrings in elementary particle physics. In noncentrosymmetric magnets, string forms of magnetic skyrmions are present as topological spin objects, and their current-induced dynamics has recently attracted intense interest. We show in the chiral magnet MnSi that the current-induced deformation dynamics of skyrmion strings results in transport response associated with the real-space Berry phase. Prominent nonlinear Hall signals emerge above the threshold current only in the skyrmion phase. We clarify the mechanism for these nonlinear Hall signals by adopting spin density wave picture to describe the moving skyrmion lattice; deformation of skyrmion strings occurs in an asymmetric manner due to the Dzyaloshinskii-Moriya interaction, which leads to the nonreciprocal nonlinear Hall response originating from an emergent electromagnetic field. This finding reveals the dynamical nature of string-like objects and consequent transport outcomes in noncentrosymmetric systems.