Greigite (Fe3S4) is a ferrimagnetic mineral with an inverse spinel structure. Besides its importance in the bio-geochemical cycle, it also has great potential applications for its unique properties such as its half metallic electronic structure at ambient condition. However, it has been challenging to get high purity and crystallinity samples of greigite in experiment, and the defect effect on the electronic structure of greigite was not clear. In the present study, first-principles calculations have been performed to investigate the ground state electronic structure of greigite with monovacancy. It is found that, with an vacancy concentration lower than 3.6%, the greigite with an Fe vacancy is an insulator with charge orderings, while the greigite with a S vacancy becomes a half-metal and has a magnetic moment of <4.0 μB per formula unit. The present result helps to understand the absence of the Verwey transition and the magnetic property of greigite measured in experiment. The understanding of the electronic structure of defective greigite could also be utilized to manipulate the properties of greigite for spintronic applications.