Abstract 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 these DM-CR 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 $b_{\chi}=0.1$ and a DM mass of $m_{\chi}=0.1~\gev$, 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 $0.1~\gev$ 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 $m_\chi\simeq 2\mev$, the effective inelastic cross-section between DM and protons must be less than $\mathcal{O}(10^{-32})~{\rm cm}^2$.