The epitaxial Pb(Zr,Ti)O3 (PZT) thin films were patterned into small islands by a photolithographic process, and the morphotropic phase boundary (MPB) in which the tetragonal and rhombohedral phases coexist was realized by changing the two-dimensional planar sizes. The MPB moved toward the Zr-rich composition due to two-dimensional film stress in the continuous epitaxial PZT thin films. The 600-nm-thick epitaxial Pb(Zr0.55Ti0.45)O3 and Pb(Zr0.60Ti0.40)O3 films were found highly rich in tetragonal phase. As the films were patterned progressively in smaller sizes and the misfit strains were relaxed further accordingly, the MPB was restored to the original bulk composition, showing higher fractions of rhombohedral phase. In the epitaxial Pb(Zr0.55Ti0.45)O3 film, two-dimensional patterns of 100×100, 10×10, and 5×5 μm2 were found within the MPB region, whereas the smallest 2×2 μm2 patterns were fully rhombohedral. On the other hand, in the epitaxial Pb(Zr0.60Ti0.40)O3 film, only the 100×100 μm2 patterns belonged to MPB rich in tetragonal phase, while the smaller patterns exhibited fully rhombohedral phases.