The gravitational baryogenesis plays an important role in the study of the baryon asymmetry. However, the original mechanism of gravitational baryogenesis in the radiation dominated era leads to the asymmetry factor η is equal to zero, which indicates this mechanism may not generate a sufficient baryon asymmetry for the standard cosmological model. In this manuscript, we investigate the gravitational baryogenesis for the generation of baryon asymmetry in the early Universe by using an new higher-order generalized uncertainty principle (GUP). It is demonstrated that the entropy and Friedman equation of the Universe deviate from the original cases due to the effect of the higherorder GUP. Those modifications break the thermal equilibrium of the Universe and in turn produces a non-zero asymmetry factor η. In particular, our results satisfy all three Sakharov conditions, which indicates that the scheme of explaining baryon asymmetry in the framework of higher-order GUP is feasible. In addition, confronting our theoretical results with the observational results, we constraint the GUP parameter β0, whose bound between 8.4 × 10 10 ∼ 1.1 × 10 13 .