Purpose The aim of the study was to study the protective effect of the Rhizoma Drynariae-Epimedium formula on osteoarthritis in rats and to explore its mechanism. Methods Fifty SD rats were randomly divided into 5 groups, namely, the control group, model group, Rhizoma Drynariae group, Epimedium group, and Rhizoma Drynariae-Epimedium group, with 10 rats in each group. Knee arthritis models were established by injecting papain solution (10% papain + 0.03 mol/L L-cysteine mixture) into the knee joint cavity of SD rats on the 0th, 3rd, and 6th days of the experiment, respectively. The model group, Rhizoma Drynariae group, Epimedium group, and Rhizoma Drynariae-Epimedium group were given modeling treatment, while the control group was not given modeling treatment. The Rhizoma Drynariae group, Epimedium group, and the Rhizoma Drynariae-Epimedium group were, respectively, given corresponding solvent gavage treatment. Both the model group and the control group were given an equal volume of normal saline. Once a day, a total of 4 w were administered. The general conditions of the rats were observed and recorded, and the knee joint width and the knee joint swelling degree of the affected side were measured and compared. HE staining and Safranin O-fast green staining were used to compare the structural changes of cartilage. The concentrations of inflammatory factors IL-1β, IL-6, and TNF-α in the joint cavity lavage fluid were determined by using ELISA. The expression of key proteins of the MAPK signaling pathway (p38, p-p38, ERK, p-ERK, JNK, and p-JNK) in joint synovial tissue was determined by western blotting. Results After modeling, except for the normal activities of the SD rats in the control group, the rest of the groups showed lack of energy and a slight limp in the knee joints. The SD rats in the model group, Rhizoma Drynariae group, Epimedium group, and Rhizoma Drynariae-Epimedium group had local swelling of the knee joint, and the knee joint width was greater than those in the control group (p < 0.05). Compared with the model group, the knee joint swelling of SD rats in the Rhizoma Drynariae group, the Epimedium group, and the Rhizoma Drynariae-Epimedium group was significantly reduced. The knee joint swelling degree of SD rats in the Rhizoma Drynariae-Epimedium group was significantly lower than that in the Rhizoma Drynariae and Epimedium groups. HE staining and Safranin O-fast green staining showed that the cartilage structure of SD rats was severely damaged and eroded, and the subchondral bone mass was reduced. Compared with the model group, the damage of cartilage tissue in the Rhizoma Drynariae group, Epimedium group, and Rhizoma Drynariae-Epimedium group was less severe. In the Rhizoma Drynariae-Epimedium group, cartilage tissue structure damage and erosion were lighter than those of the Rhizoma Drynariae group and the Epimedium group. The concentrations of inflammatory factors IL-1β, IL-6, and TNF-α in the articular cavity lavage fluid of SD rats in the model group, Rhizoma Drynariae group, Epimedium group, and Rhizoma Drynariae-Epimedium group were higher than those in the control group. Compared with the model group, the concentrations of IL-1β, IL-6, and TNF-α in the joint cavity lavage fluid of the Rhizoma Drynariae group, Epimedium group, and Rhizoma Drynariae-Epimedium group were significantly decreased. In the Rhizoma Drynariae-Epimedium group, IL-1β, IL-6, and TNF-α concentrations were lower than those of the Rhizoma Drynariae and Epimedium groups. Compared with the control group, the expression levels of p-p38, p-ERK, and p-JNK proteins in the model group, Rhizoma Drynariae group, Epimedium group, and Rhizoma Drynariae-Epimedium group were significantly increased. The expression levels of p-ERK, p-p38 and p-JNK in the Drynariae group, Epimedium group, and Drynariae-Epimedium group were significantly lower than those in the model group. The expression levels of p-ERK, p-p38, and p-JNK in the Rhizoma Drynariae-Epimedium group were significantly lower than those in the Rhizoma Drynariae and Epimedium groups. Conclusion The Rhizoma Drynariae-Epimedium formula can play a protective role in the process of osteoarthritis by inhibiting the phosphorylation levels of p38, ERK, and JNK-related proteins in the cartilage tissue MAPK signaling pathway, reducing the inflammatory response.