Adipose derived stem cells (ADSCs) have the potential to attenuate osteoarthritis (OA); however, complications such as immune rejection and tumour formation limit their application. Exosomes (Exos)-mediated acellular therapy is promising in alleviating OA. This study aims to confirm whether ADSC-exos derived from infrapatellar fat pad (IPFP, ExosIPFP) are more suitable for ameliorating OA than ADSC-exos derived from subcutaneous fat (ScAT, ExoScAT) in vitro and in DMM models. Then, we investigated the regulatory mechanism by which the two kinds of Exos inhibit extracellular matrix (ECM) degradation in OA. ADSCs were successfully isolated and Exos were then obtained. ExosIPFP exhibited better attenuated effects on osteoarthritic chondrocytes in vitro and in vivo than ExoScAT. Small RNA sequencing was performed and the results shown that miR-99b-3p was upregulated in ExosIPFP. In vitro experiments confirmed that ADAMTS4 is a direct downstream target of miR-99b-3p. Over-expression miR-99b-3p in ExosScAT (ExosScAT-99b-3p) indicated that miR-99b-3p serves a positive role for OA treatment by inhibiting ADAMTS4 expression both in vitro and in vivo. In addition, hydrogel microparticles (HMPs) system was prepared by microfluidic technology, and confirmed the beneficial results for long-term therapeutic by continuous release of Exos. Take together, these results suggest that the therapeutic effects of ADSC-Exos may vary according to differential expression of miRNAs. Exosomal miR-99b-3p may act as a promising therapeutic strategy for OA, in addition, the injectable HMPs act as a sustained local drug release system, therefore representing great potential for treating OA and other diseases.