Phase has emerged as an important structural parameter — in addition to composition, morphology, architecture, facet, size and dimensionality — that determines the properties and functionalities of nanomaterials. In particular, unconventional phases in nanomaterials that are unattainable in the bulk state can potentially endow nanomaterials with intriguing properties and innovative applications. Great progress has been made in the phase engineering of nanomaterials (PEN), including synthesis of nanomaterials with unconventional phases and phase transformation of nanomaterials. This Review provides an overview on the recent progress in PEN. We discuss various strategies used to synthesize nanomaterials with unconventional phases and induce phase transformation of nanomaterials, by taking noble metals and layered transition metal dichalcogenides as typical examples. Moreover, we also highlight recent advances in the preparation of amorphous nanomaterials, amorphous–crystalline and crystal phase-based hetero-nanostructures. We also provide personal perspectives on challenges and opportunities in this emerging field, including exploration of phase-dependent properties and applications, rational design of phase-based heterostructures and extension of the concept of phase engineering to a wider range of materials.