The direct detection of particle dark matter through its scattering with nucleons is of fundamental importance to understand the nature of dark matter. In our recent work 2004.03161, we proposed that the high-energy neutrino detectors like IceCube can be used to uniquely probe the dark matter -- nucleon cross-section for high-energy DM of ~ PeV, up-scattered by the high-energy cosmic rays. We derive for the first time constraints on the dark matter -- nucleon cross-section down to ~ 10^-32 cm^2 at this energy scale for sub-GeV dark matter. Such independent probe at energy exceeding other existing direct detection experiments can provide useful insights complementary to other searches.