We demonstrated ion exchange (hydration and dehydration) in the perfect (010)-oriented growth of Dion–Jacobson perovskite RbLaNb2O7 thin films prepared by ELAMOD. The hydration of the RbLaNb2O7 thin film immediately proceeded in an acid solution at room temperature, and the obtained HLaNb2O7·0.5H2O film was rapidly dehydrated by low-temperature heating at 250°C. The hydrated HLaNb2O7·0.5H2O and dehydrated HLaNb2O7 films rigidly kept their uniaxial ordering to the substrate normal. Furthermore, their surface roughness decreased by 25% and the X-ray reflection peak width of their χ profile also decreased by 24% throughout the ion exchange. These improvements in the surface roughness and orientation quality of the seed layer enhanced the orientation growth and conducting property of the LaNiO3 film on the seed layer. The ρ of the LaNiO3 film on the protonated HLaNb2O7 seed layer was 0.79 mΩ·cm, which was 30% lower than that of the film on the original RbLaNb2O7 seed layer. Thus, we confirmed that the ion-exchange protonation of a RbLaNb2O7 seed layer prepared by ELAMOD is effective in improving seed layer properties.