This study presents a clinical treatment decision support system (CTDSS) through which clinicians can simplify the shared-decision making (SDM) process for treating knee osteoarthritis (OA). This system enables patients to participate in selecting the optimum treatment. There has been broad international acceptance of SDM, but its practical implementation in clinical setting has posed challenges. The proposed method incorporates analytic hierarchy process and fuzzy multi-choice goal programming (AHP-FMCGP) into CTDSS to determine treatment standards, beginning with a literature review and expert surveys. The method provides patients with flexibility to modify treatment goals and constraints during the decision-making (DM) process to achieve their preferred treatment and simplifying the traditional SDM. A total of 240 knee OA patients participated in this pilot study, and the results indicated a significant improvement in patient satisfaction (F = 4.104; P < 0.05) with the implementation of CTDSS. This study demonstrates the effectiveness of CTDSS by resolving several challenges in clinical implementation: (1) Improved efficiency of implementing SDM, promoting better clinician-patient communication and higher healthcare quality. (2) Eliminating the need for extensive health literacy and disease knowledge in patients during the DM process. (3) Saving time for physicians, by allowing them to better understand the patients’ preferences and select the most appropriate treatment option. (4) This method can be extended to primary clinics to benefit other patients.