An incommensurate phase refers to a solid state in which the period of a superstructure is incommensurable with the primitive unit cell. Recently the incommensurate phase is induced by applying an in-plane strain to hexagonal manganites, which demonstrates single chiral modulation of six domain variants. Here we employ Landau theory in combination with the phase-field method to investigate the incommensurate phase in hexagonal manganites. It is shown that the equilibrium wave length of the incommensurate phase is determined by temperature and the magnitude of the applied strain, and a temperature-strain phase diagram is constructed for the stability of the incommensurate phase. Temporal evolution of domain structures reveals that the applied strain not only produces the force pulling the vortices and anti-vortices in opposite directions, but also results in the creation and annihilation of vortex-antivortex pairs.