This work derived the relationship between the concentrations of Pb²⁺ and I⁻ vacancies, along with MA⁺ vacancies, in MAPbI₃ crystals and their effect on the short-circuit current of MAPbI₃-based solar photovoltaic devices. First principles calculations revealed that Pb²⁺ and I⁻ vacancies introduce shallow defect levels near the Fermi level, acting as non-radiative recombination centers, which significantly influence the short-circuit current and open-circuit voltage. In contrast, MA⁺ vacancies have a negligible effect on the optoelectronic properties of MAPbI₃. Based on this correlation, we successfully elucidated the declining trend of the short-circuit current (J_sc) in MAPbI₃-based devices with increasing Pb²⁺/I⁻ vacancy concentrations, while uncovering the microscopic mechanism responsible for the minor performance impact of MA⁺ vacancies.