An efficient and durable utilization of light to drive photocatalytic reactions still requires the overcoming of barriers. Herein, two-dimensional (2D) ultrathin IL_Bi2WO6 (IL_BWO) photocatalysts were prepared for the first time via ionic liquid-assisted hydrothermal route by adjusting the amount of tetrabutylammonium chloride [TBA][Cl], synthesis temperature and duration. IL played the role of morphology-directing agent given by selecting the amount of IL, the control of nanosheet thickness was possible. The replacement of IL with KCl resulted in the growth of similar nanostructure, but with higher thickness, while, the absence of Cl− caused the formation of clew-like microspheres. Two different model experiments, phenol degradation, and inactivation of Escherichia coli and Staphylococcus aureus bacteria were chosen to evaluate the photocatalytic activity. The improved photocatalytic performance was attributed to (i) the ultrathin structure, which let for shorter diffusion distance, (ii) the nitrogen presence in the photocatalyst structure, and (iii) the oxygen vacancies formation. The •OH and h+ were the main species involved in the mechanism of photooxidation, and could be also responsible for the enhanced antimicrobial properties. The unique strategy of IL application establishes a new insight for a controllable preparation of 2D Bi2WO6 with improvement photocatalytic and antibacterial properties.