Phototheranostics that concurrently and complementarily integrate real‐time diagnosis and in situ therapeutic capabilities in one platform has become the advancing edge of precision medicine. Organic agents possess the merits of facile preparation, high purity, tunable photophysical property, good biocompatibility, and potential biodegradability, which have shown great promise for disease theranostics. This review summarizes the recent achievements of organic phototheranostic agents and applications, especially which rationally utilize energy dissipation pathways of Jablonski diagram to modulate the fluorescence emission, photoacoustic/photothermal production, and photodynamic processes. Of particular interest are the systems exhibiting huge differences in aggregate state as compared with the solution or single molecule form, during which the intramolecular motions play an important role in regulating the photophysical properties. The recent advances from such an aspect for biomedical applications including high‐resolution imaging, activatable imaging and therapy, adaptive theranostics, image‐guided surgery, immunotherapy, and afterglow imaging are discussed. A brief summary and perspective in this field are also presented. We hope this review will be helpful to the researchers interested in bioprobe design and theranostic applications, and inspire new insights into the linkage between aggregate science and biomedical field.