We investigate the flux flow state in a two-gap superconductor in which two s-wave gaps with different amplitudes exist on two separate Fermi surfaces. The flux flow resistivity is obtained on the basis of the Bardeen-Stephen relation and the result agrees well with the anomalous field dependence of the flow resistivity recently observed in the two-gap superconductor MgB2. Some typical properties of the vortex in this system are also discussed.