(111¯)/(111)-oriented rhombohedral Pb(Zr0.65Ti0.35)O3 films with different domain fractions were epitaxially grown on various single crystals. The volume fraction of (111)-polar-axis oriented domains in as-deposited films, Vpol.(as-depo.), was controlled by selecting a single crystal substrate with a different thermal expansion coefficient. Applying an electric field, referred to as “poling treatment”, resulted in irreversible non-180° domain switching from the (111¯)-oriented domain (non-polar-axis) to the (111)-oriented domain (polar-axis), which was observed by synchrotron X-ray diffraction. Remanent polarization (Pr) values were higher than those estimated using the proportional relationship with Vpol.(as-depo.). However, the experimental Pr values were in good agreement with the values estimated using the volume fraction of (111)-oriented domains after applying the poling treatment. In rhombohedral Pb(Zr0.65Ti0.35)O3 films, 30%−50% of the (111¯)-oriented domains switched irreversibly to (111)-oriented domains as a result of the poling treatment. The present results show that the domain structures of films may change dramatically after the poling process, and both before and after the poling state should be characterized in order to interpret polarization and piezoelectric behaviors. This study helps to clarify the ferroelectric and piezoelectric properties of Pb(Zr, Ti)O3 films after poling treatment.