Two-dimensional (2D) nanomaterials have attracted increasing interest because of their compelling physicochemical properties and promising applications. Recent studies have demonstrated that phases of nanomaterials could significantly affect their properties and applications because of the distinct atomic arrangements. Besides crystalline phases, the amorphous nanomaterials, which lack long-range atomic ordering, and heterophase nanostructures consisting of more than one phase have also shown enhanced performances in some specific applications. Recently, with the rapid development in phase engineering of nanomaterials (PEN), the controlled synthesis of 2D nanomaterials with unconventional phases and the exploration of phase-dependent properties and applications have been witnessed. In this perspective, we briefly summarize the research progress on 2D nanomaterials with unconventional phases, including unconventional crystal phases, amorphous phase, and heterophase. On the basis of different material categories, we highlight their synthetic methodologies, unique structures, and intriguing properties. Finally, we provide personal insights on challenges and potential research opportunities in this emerging field.