Ferroelectric materials are widely used in the applications of electronic devices due to their robust spontaneous polarization. The surface roughness of ferroelectric thin films, which is closely related to the morphology, can play an important role in determining the ferroelectric domain structures. In this work, we have investigated the influence of annealing conditions on the surface morphology of epitaxial BiFeO₃ and SrRuO₃ thin films prepared by pulsed laser deposition on SrTiO₃ (001) substrates. It is found that the morphology of the thin films is sensitive to the annealing time and cooling rate, and the corresponding surface roughness decreases with increasing annealing time and decreasing cooling rate. In addition, the ferroelectric domain structures of BiFeO₃ films have been investigated by piezoelectric force microscopy, which shows a significant improvement in domain size and reverse piezoelectric response in the thin films with decreasing surface roughness. This work provides a simple way to predict and improve the ferroelectric domain structures by in situ annealing.