Because of the dense environment, neutron stars (NSs) can serve as an ideal laboratory for studying the interactions between dark matter (DM) and ordinary matter. In the process of DM capture, deep inelastic scattering may dominate over elastic scattering, especially for the DM with a large momentum transfer. In this work, we calculate DM-nucleon deep inelastic scattering via a vector mediator and estimate its contribution to the capture rate. Using the surface temperature of the NSs, we derive the exclusion limits for the DM-nucleon scattering cross section in the mass range 1 GeV<mχ<105 GeV. We find the bounds for DM with the mass ≳1 GeV can be changed several times after including the deep inelastic scattering contribution. Published by the American Physical Society 2024