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This study assesses inpatients’ preferences for participating in medical decision-making and determines the factors’ rankings in order of importance and whether they vary for respondents with different characteristics. Case 1 best-worst scaling (BWS) was used for the study design. Thirteen attributes influencing inpatient medical decision-making participation were identified based on a literature review and interview results. A balanced incomplete block design was used to form choice sets for the BWS questionnaire for a cross-sectional study examining inpatients’ preferences for participating in medical decision-making. Based on results from 814 inpatient participants, the three most important factors influencing inpatients’ medical decision-making participation were inpatients’ trust in physicians, physicians’ professional expertise, and physicians’ attitudes. The mixed logit model results reflect the significant heterogeneity in respondents’ preferences for shared decision-making. To facilitate resource allocation, improve the physician-patient relationship, and encourage patient decision-making participation more actively and effectively, decision-makers should emphasize patients’ trust, enhance physicians’ ability to diagnose and treat diseases, and improve their attitudes toward providing care and communication from the perspectives of patients, physicians, and the social environment. Further research is needed on the heterogeneity of patients’ preferences for participating in medical decision-making and how to improve patient participation.