Evidence accumulated that mesenchymal stem cell (MSC) therapy ameliorated osteoarthritis (OA) via paracrine effect, whereas conditioned medium (CM) of MSCs contains all the secretomes. In vitro studies have proved its therapeutic effect in OA, but few in vivo evidences were unveiled. This study investigated the effect of MSCsâCM in an animal model of OA. OA was induced by anterior cruciate ligament transaction and destabilization of the medial meniscus in 12 rats bilaterally. The CM group (N = 6) was administered with intraarticular injection of MSCsâCM weekly, whereas the phosphateâbuffered saline (PBS) group (N = 6) was injected with PBS. Six rats served as normal control and received sham operation with weekly PBS injection. Rats were sacrificed 8 weeks postoperatively. Gross and histological morphology were analysed. Microcomputed tomography was applied to assess the subchondral bone. Components of extracellular matrix (ECM) including type II collagen (Col II) and aggrecan, and ECM homeostasisârelated enzymes (metalloproteinaseâ13 [MMPâ13] and tissue inhibitor of metalloproteinaseâ1 [TIMPâ1]), as well as autophagy markers (Beclinâ1 and microtubuleâassociated protein light chain 3) were evaluated immunohistochemically. Chondrocyte apoptosis was measured by terminal deoxynucleotidyl transferase dUTP nickâend labelling staining. Gene expression of Col II, aggrecan, MMPâ13, and TIMPâ1 was confirmed by realâtime polymerase chain reaction. Morphological outcomes demonstrated remarkable articularâprotective effect of MSCsâCM. Wellâmaintained subchondral bone structure, significantly more abundant cartilage matrix, notably decreased ratio of MMPâ13 to TIMPâ1, and inhibited chondrocyte apoptosis with enhanced autophagy were observed in the CM group compared with the PBS group. In conclusion, MSCsâCM demonstrated satisfactory effect in alleviating OA in rats via protecting the microarchitecture of subchondral bone, balancing the ratio of MMPâ13 to TIMPâ1 in cartilage, and enhancing autophagy, which might provide a new remedy against OA.