In this study, two kinds of gas cluster ion beam energy modes with different ion dose ratios are proposed to improve the traumatic surface of n-Si (100) single crystal. In mode1, low-dose high-energy clusters and high-dose low-energy clusters are used, while in mode2, high-dose high-energy clusters and low-dose low-energy clusters are used. The results show that the flattening effect of mode 1 is better than that of mode 2, and the root mean square roughness of mode 1 and mode 2 are 0.62 nm and 1.02 nm, respectively. This is because in multi-level energy mode 2, high-dose high-energy clusters are used to bombard the target surface in the early stage, so that more ion damages will be left after high-energy cluster bombardment. In the later stage, low-dose low-energy clusters can only remove part of the ion damages, and the repair strength is not strong enough. In multi-level energy mode1, we first use low-dose high-energy clusters to bombard the surface of the target, so that the high-energy clusters can quickly remove the shape objects with high protrusion on the sample surface, and in the low-dose mode, it will not leave too many ion damages, which is conducive to the later repair. In the first stage of multi-level energy mode, high-dose low-energy clusters are used to bombard the target surface, which can not only reduce the ion loss, but also increase the time for low-energy clusters to repair ion damages, thereby yielding the optimal flattening effect. In order to verify the relationship among the damage removal, ion damage degree and cluster energy, a single energy cluster bombardment experiment with mechanical damage is carried out before the multi-level energy mode modification is studied. The results show that when the cluster ions are accelerated at 15 kV high voltage, the scratch removal efficiency is highest, and the surface scratch is very shallow, but the decease of roughness is not obvious; when the cluster ions are accelerated at 8 kV and 5 kV, the sample surface becomes fine and the remaining ion damages are least. At the same time, a comparison of the target bombarded by the multi-level energy mode 1 clusters with that by the single energy clusters shows that the multi-level energy mode can obtain a smoother target surface than the single 15 keV high-energy cluster treatment; the multi-level energy mode can better remove scratches and other wounds than the single 5 keV low-energy cluster treatment. Multistage energy mode 1 integrates the advantages of high and low energy clusters, thereby achieving the best flattening effect.