Phototherapy based on micro light-emitting diodes (µLEDs) has gained enormous attention in the medical field as a patient-friendly therapeutic method due to its advantages of minimal invasiveness, fewer side effects, and versatile device form factors with high stability in biological environment. Effective cosmetic and medical phototherapy depends on deep light penetration, precise irradiation, and simultaneous multi-site stimulation, facilitated by three-dimensional (3D) optoelectronics specifically designed for complex human matters, defined here as 3D µLEDs. This perspective article aims to present the functionalities and strategies of 3D µLEDs for human-centric phototherapy. This study investigates the effectiveness of phototherapy enabled by three key functionalities such as shape morphing, self-adaptation, and multilayered spatiotemporal mapping of 3D µLEDs. Finally, this article provides future insights of 3D µLEDs for human-centric phototherapy applications.