Regenerating natural gradients of the tendon‒bone interface (TBI) is a major challenge in the reconstruction of rotator cuff tear (RCT). In this study, magnetic Janus hydrogel microrobots to match the TBI orientation during RCT reconstruction surgery are developed via a biofriendly gas-shearing microfluidic platform. Through separate loading of Mg2+ and Zn2+, the microrobots facilitate the immediate restoration and long-term maintenance of the natural mineral gradient in the TBI after implantation and alignment through magnetic manipulation. In vitro studies confirm the spatiotemporal cell phenotype modulation effects of the microrobots. In a rat RCT model, microrobots synchronously promote the bone and tendon regeneration, and the restoration of gradient tendon‒bone transition structures in the TBI. Overall, by rebuilding the Mg2+/Zn2+ mineral gradient, cell phenotype gradient and structural gradient of the TBI, magnetic Janus microrobots loaded with dual bioactive ions represent a promising strategy for promoting TBI healing in RCT reconstruction surgery.