We investigate the impact of inelastic collisions between dark matter (DM) and heavy cosmic ray (CR) nuclei on CR propagation. We approximate the fragmentation cross-sections for DM-CR collisions using collider-measured proton-nuclei scattering cross-sections, allowing us to assess how these collisions affect the spectra of CR boron and carbon. We derive new CR spectra from DM-CR collisions by incorporating their cross-sections into the source terms and solving the diffusion equation for the complete network of reactions involved in generating secondary species. In a specific example with a coupling strength of b χ = 0.1 and a DM mass of m χ = 0.1 GeV, considering a simplified scenario where DM interacts exclusively with oxygen, a notable modification in the boron-to-carbon spectrum due to the DM-CR interaction is observed. Particularly, the peak within the spectrum, spanning from 0.1 to 10 GeV, experiences an enhancement of approximately 1.5 times. However, in a more realistic scenario where DM particles interact with all CRs, this peak can be amplified to twice its original value. Utilizing the latest data from AMS-02 and DAMPE on the boron-to-carbon ratio, we estimate a 95% upper limit for the effective inelastic cross-section of DM-proton as a function of DM mass. Our findings reveal that at m χ ≃ 2 MeV, the effective inelastic cross-section between DM and protons must be less than O(10−32)cm2 .