The dependence of the L10 ordering, magnetic properties and microstructure on film thickness of the Fe51Pd49 nanoparticle films deposited at 800 °C was investigated. The L10 ordered phase and hard magnetic properties were found for the samples with the thickness less than 30 nm. As the thickness was increased to 45 nm and thicker, the samples exhibited the A1 disordered phase and soft magnetic properties. The lack of heterogeneous nucleation sites is responsible for the A1 disordered phase in the thicker FePd samples, which was confirmed by the results of microstructural and crystallographic analyses. The long term re-annealing at a lower temperature (600 °C for 8 h) can induce the L10 ordering of the large size FePd nanoparticles originally composed of the A1 phase, which also supports the statement that the heterogeneous nucleation sites play an important role on L10 ordering of the FePd films.