Measurement of neutron energy spectrum is very important to develop the application of neutrons in different fields of science and technology. One of the commonly used methods to measure the neutron energy spectrum is the threshold foil activation method and using an unfolding code such as SAND-II. The main limitation of such codes is that the geometry of the source and measurement setup could not be defined in the code. The main objective of this study is the coupling SAND-II and MCNPX codes to consider the geometry effect on the unfolded neutron energy spectrum. The full geometry of the measurement setup including the source and foils can be simulated by MCNPX code. The results show that considering the irradiation geometry produces a better a-priori information of the neutron field.