The crystallization of FePt/MgO(001) magnetic thin films of various thicknesses has been studied using synchrotron x-ray scattering, atomic force microscope, and vibrating sample magnetometer. In film with a 499-$AA$-thick, face-centered tetragonal, ordered FePt phase was dominantly crystallized into perpendicular (001) grains keeping the magnetically easy c-axis normal to the film plane during annealing. In film with a 816-$AA$-thick, however, longitudinal (110) grains keeping the c-axis parallel to the film plane were grown on top of the perpendicular (001) grains. The behavior of the magnetic properties was consistent with the thickness dependence of the crystallization. We attribute the thickness dependence of the crystallization to the substrate effect, which prefers the growth of the c-axis oriented perpendicular grains near the film/substrate interfacial area.