The FePt thin films with [Fe/Pt] multilayer structure have been prepared on preheated Corning 1737F glass substrate using pure Fe and Pt target in a CMS-18 sputtering system. The dependence of FePt's perpendicular anisotropy on the multilayer structure was investigated. It was found that the perpendicular coercivity and remanence ratio could be enhanced in the FePt films by an optimization of the multilayer structure. The mechanism of the perpendicular anisotropy in [Fe/Pt] multilayer films was analyzed using the micromagnetic models, with careful discussions of the crystalline and interface anisotropies. It was found that the Fe/Pt interfaces play an important role in favoring the perpendicular orientation in the [Fe/Pt] multilayer films.