Microalloying plays a critical role in improving the mechanical properties of steel. To offer a better theoretical guide for experimental research at the atomic level, this paper investigated the synergistic mechanism of adding trace amounts of alloy Cr and Ni and the microstructure evolution of nanocrystalline ferrite during the mechanical response process. First-principles calculations were implemented to investigate electronic properties. Hybrid molecular dynamics and Monte Carlo simulations were employed to explore the deformation mechanism under uniaxial tension and scratching. Specifically, comprehensive differences between doped and pure nanocrystalline ferrites were explored regarding local stress-strain state, dislocation evolution, twin expansion, and grain boundary activity. The results show that Cr- and Ni-doped nanocrystalline ferrite has higher strength and better wear resistance. The potential mechanism is that the addition of Cr and Ni enhances the atomic bonding strength with Fe atoms, hinders the movement of dislocations caused by lattice distortion, and suppresses grain boundary slip and migration, thereby improving the resistance to plastic deformation and grain boundary stability. Theoretical calculations based on microstructure indicate that compared to solid solution strengthening, Ni-induced grain boundary strengthening plays a dominant role in improving yield strength. Under large deformation, the trend of mechanical response is reversed. The suppression of dislocation motion by Cr reduces the dislocation density and dislocation entanglement, resulting in flow stress and local scratch force being smaller than that of pure samples. However, the formation of more nanoscale twins and twin-dislocation interactions enhances strain-hardening ability during tensile. Finer nanostructured subgrains are formed under scratching. These results provide valuable insights into the understanding of the strengthening mechanism and plastic deformation mechanism of Cr-Ni system low alloy steel under dynamic loading.