Based on the Geant4 program-the package for simulating particle transportation in materials, simulations of the irradiation by neutrons with 1 MeV energy in zirconium were conducted The two adjacent elastic collisions between injected neutron and target atoms produce numerous primary knock-on atoms (PKA). It is found that the average distance of adjacent collisions is 29.47 mm, and the kinetic energy of most PKAs ranges from 1 keV to 15 keV. The damaged area induced by the PKAs is in nanometer scale, which is far less than the distance between the two PKAs. According to the fact that, the subsequent cascade collisions caused by the two PKAs can be considered as a set of independent processes, it is reasonable to study the cascade collisions of the PKAs by means of molecular dynamics method. The cascade collision progress of PKAs with different energies was performed, and the number of interstitial atoms and the size of the damaged regions in the material were extracted. Through the combination of Monte Carlo method and molecular dynamics simulation, a complete physical picture of the primary damage caused by the 1 MeV neutrons in the zirconium was obtained.