In order to investigate the modification of the surface structure of FePS3 via Ga+ ion irradiation, we study the effect of thickness and Raman spectrum of multilayer FePS3 irradiated for 0 μs, 30 μs, and 40 μs, respectively. The results demonstrate that the intensity ratio of characteristic Raman peaks are obviously related to the thickness of FePS3. After Ga+ ion irradiation, the FePS3 sample gradually became thinner and the Eu peak and Eg(v11) peak in the Raman spectrum disappeared and the peak intensity ratio of A1g(v2) with respect to A1g(v1) weakened. This trend becomes more apparent while increasing irradiation time. The phenomenon is attributed to the damage of bipyramid structure of [P2S6]4− units and the cleavage of the P-P bands and the P-S bands during Ga+ ion irradiation. The results are of great significance for improving the two-dimensional characteristics of FePS3 by Ga+ ion beam, including structural and optical properties, which pave the way of surface engineering to improve the performance of various two-dimensional layered materials via ion beam irradiation.