Various magnetic microcarrier systems capable of transporting cells to target lesions are developed for therapeutic agent-based tissue regeneration. However, the need for bioactive molecules and cells, the potential toxicity of the microcarrier, and the large volume and limited workspace of the magnetic targeting device remain challenging issues associated with microcarrier systems. Here, a multifunctional magnetic implant system is presented for targeted delivery, secure fixation, and induced differentiation of stem cells. This magnetic implant system consists of a biomaterial-based microcarrier containing bioactive molecules, a portable magnet array device, and a biocompatible paramagnetic implant. Among biomedical applications, the magnetic implant system is developed for knee cartilage repair. The various functions of these components are verified through in vitro, phantom, and ex vivo tests. As a result, a single microcarrier can load ≈1.52 ng of transforming growth factor (TGF-1) and 3.3 × 10 3 of stem cells and stimulate chondrogenic differentiation without extra bioactive molecule administration. Additionally, the implant system demonstrates high targeting efficiency (over 90%) of the microcarriers in a knee phantom and ex vivo pig knee joint. The results show that this implant system, which overcomes the limitations of the existing magnetic targeting system, represents an important advancement in the field.