The construction of visible-light-driven hybrid heterostructure photocatalysts is of great significance for environmental remediation, although the utilization of strong visible-light response photocatalysts with high efficiency and stability remains a major challenge. On the other hand, defect engineering is an excellent way to introduce metal cation vacancies in materials, thereby ensuing in highly enhanced catalytic performance. Inspired by this, we effectively constructed a built-in interface α-MnO2/Bi2WO6 heterostructure with abundant intimate interfaces and defective Mn3+/Mn4+ active sites for photocatalytic tetracycline hydrochloride (TC-HCl), hexavalent chromium Cr6+ reduction, and Escherichia coli (E. coli) inactivation. The experimental results, such as the active species test and X-ray photoelectron spectroscopy, indicated that the defective sites Mn3+/Mn4+, surface oxygen vacancies, and Bi(3+x)+ boosted the visible light absorption, and highly enhanced the photoinduced charge separation/transfer. Furthermore, experimental and DFT calculations reveal the high charge density at the built-in interface heterostructure and the Z-scheme charge transfer mechanism during the photocatalytic process. The results further reveal that O2− and 1O2 are the main reactive active species contributing to the photocatalytic reaction. The exceptional TC-HCl decomposition activity of the α-MnO2/Bi2WO6 heterostructure (97.56%, 2.31, and 2.04 times higher than bulk), enhanced reaction kinetics (Kapp = 0.041 min−1, 6.4, and 5.2 times higher than bulk), removal rate of 80.3%, Cr6+ reduction to Cr3+ (98.56%, Kapp = 0.0599 min−1), and almost 100% bacterial inactivation compared to bulk α-MnO2 (42.22%) and Bi2WO6 (47.76%), were mainly due to the enhanced charge separation/transfer at the built-in interface and high charge density. This study opens new horizons for constructing Z-scheme MnO-based interface heterostructures with abundant defect sites for exceptional photocatalytic applications.