In this paper, the evolution of vortex configuration for mesoscopic two-gap superconductor is investigated by the time-dependent Ginzburg-Landau theory in the presence of an externally applied field. The vortex configurations of s-wave and d-wave, and the distribution of magnetic field are given when the temperature is between critical temperatures of s-wave and d-wave. In theory, the over-cold and the over-hot field, and the boundary effect on vortex are simulated when the magnetic flux penetrates the superconductor.