Upconversion (UC) nanostructures, which can upconvert near-infrared (NIR) light with low energy to visible or UV light with higher energy, are investigated for theranostic applications. The surface of lanthanide (Ln)-doped UC nanostructures can be modified with different functional groups and bioconjugated with biomolecules for therapeutic systems. On the other hand, organic molecular-based UC nanostructures, by using the triplet-triplet annihilation (TTA) UC mechanism, have high UC quantum yields and do not require high excitation power. In this review, the major UC mechanisms in different nanostructures have been introduced, including the Ln-doped UC mechanism and the TTA UC mechanism. The design and fabrication of Ln-doped UC nanostructures and TTA UC-based UC nanostructures for theranostic applications have been reviewed and discussed. In addition, the current progress in the application of UC nanostructures for diagnosis and therapy has been summarized, including tumor-targeted bioimaging and chemotherapy, image-guided diagnosis and phototherapy, NIR-triggered controlled drug releasing and bioimaging. We also provide insight into the development of emerging UC nanostructures in the field of theranostics.