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The effect of the divacancy defect on magnetic properties of Fe94V6 alloys was investigated using the first-principles calculations based on density functional theory. The model of Fe28V2 super-lattice for a divacancy in Fe94V6 alloy was established, in comparison with the perfect Fe30V2 super-lattice. For the first time, the effect of the on-site Coulomb repulsion term was considered to correct the underestimation for the bandgap. The magnetism of the Fe, V atoms, and the super-lattice were analyzed by the electron hybridization of the atoms, and the interactions between V and four different neighboring Fe atoms were also investigated. The results show that both Fe28V2 and Fe30V2 super-lattices are ferromagnetic, which is determined mainly by the strong ferromagnetism of Fe 3d electrons, and the hybridizations between Fe 3d electrons and Fe 2p and V 3d electrons account for the weak anti-ferromagnetism. When the Fe divacancy exists, the average magnetic moments of the Fe28V2 super-lattice and Fe atoms inside increase, while that of V atoms decreases due to the change of the Fe-V charges. The variation of the magnetic moments of different neighboring Fe atoms with respect to V atoms depends on the charge transfer and the Fe-V interaction.