The even single phase β-FeSi2 thin films were prepared by femtosecond pulsed laser deposition (PLD) on Si(111) wafers at different temperature using an FeSi2 alloy target, and excimer (nanosecond) PLD was introduced to prepared β-FeSi2 thin films also. X-ray diffraction (XRD), field scanning electron microscopy (FSEM), energy disperse spectroscopy (EDS), ultraviolet-visible spectra photometer were used to characterize the structure, composition and morphology of the films. The micro drop appeared in the both samples prepared by nanosecond PLD at 500 ℃ and 550 ℃, the maze surface appeared in the surface of the sample prepared at 550 ℃. The single phase β-FeSi2 thin films were gained by femtosecond PLD below 400 ℃, but the proper temperature of nanosecond PLD was 500 ℃; The β-FeSi2 thin films prepared by femtosecond PLD were free of micro drop, the deposition efficiency at unit average laser power in the process of depositing β-FeSi2 thin films by the femtosecond PLD system was 1000 times over that of the nanosecond PLD system.