The effective removal of organic pollutants and bacteria are of great significance considering the hazards to the environment and human health. The two-dimensional AgBiO₃/Bi₂MoO₆ heterojunction with rich oxygen vacancies was successfully fabricated via a hydrothermal method and systematically characterized by various analytical techniques. The photocatalytic experimental results revealed that the addition of AgBiO₃ improved the photocatalytic performance of Bi₂MoO₆, and the AgBiO₃/Bi₂MoO₆-10 heterojunction possessed the best degradation effect toward RhB (72%) within 100 min, with 1.38 and 1.44 times higher activity than pure Bi₂MoO₆ and AgBiO₃, respectively. The bacteria were completely inactivated within 90 min by AgBiO₃/Bi₂MoO₆-10 heterojunction. The reason for the enhancement of photocatalytic activity was the synergistic effect between AgBiO₃ and Bi₂MoO₆. The constructed Z-scheme heterojunction with oxygen vacancies improved the separation efficiency of photo-induced electrons and holes and broadened the range of visible-light absorption. The trapping experiments and ESR indicated that superoxide radical and holes were the main reactive species.