As the important structure elements, vacancies are believed to be a crucial factor in the composite multiferroics. In the work, first-principles calculations have been performed to study the effect of vacancies (O, Ti) on the structural, magnetoelectric and electronic properties of the Fe/BaTiO3 interface. The vacancy-type defects are introduced in the first interfacial TiO2 layer. It is found that the interfacial vacancies (O, Ti) will increase the bonding strength of the ferromagnetic/ferroelectric system while the magnetoelectric effect can still keep the same order of magnitude as perfect Fe/BaTiO3, which may be helpful for designing multiferroic thin film materials.