Abstract In this paper, a novel bioinspired stem cell‐laden microgel and related in vivo cartilage repair strategy are proposed. In particular, herein the preparation of new stem cell‐laden microgels, which can be injected into the chondral defect site in a minimally invasive way, and more importantly, capable of in situ self‐assembly into 3D macroporous scaffold without external stimuli, is presented. Specifically, thiolated gelatin (Gel‐SH) and vinyl sulfonated hyaluronic acid (HA‐VS) are first synthesized, and then stem cell‐laden gelatin/hyaluronic acid hybrid microgels (Gel‐HA) are generated by mixing Gel‐SH, HA‐VS, and bone mesenchymal stem cells (BMSCs) together via droplet‐based microfluidic approach, followed by gelation through fast and efficient thiol‐Michael addition reaction. The encapsulated BMSCs show high viability, proliferation, and chondrogenic differentiation potential in the microgels. Moreover, the in vitro test proves that BMSC‐laden Gel‐HA microgels are injectable without sacrificing BMSC viability, and more importantly, can self‐assemble into cartilage‐like scaffolds via cell–cell interconnectivity. In vivo experiments further confirm that the self‐assembled microgels can inhibit vascularization and hypertrophy. The Gel‐HA microgels and relevant cartilage repair strategy, i.e., injecting BMSC‐laden microgels separately and reconstructing chondral defect structure by microgel self‐assembly, provides a simple and effective method for cartilage tissue engineering and regenerative medicine.