Background: Primary health care (PHC) is a key component of the health care system in many countries. In China, however, PHC institutions are less preferred by patients, leading to the underuse of PHC services. Factors affecting patients’ preferences for PHC institutions in China remain unreported in the current literature, which was first explored in this study. Method: A qualitative interview study was conducted in Nanjing, Jiangsu Province of China. A semi-structured interview guide was applied to ask patients’ opinions regarding the PHC institutions in China. Qualitative data analysis was conducted using the thematic framework approach. Results: A total of 142 participants were interviewed. Three themes and their sub-themes emerged from the study: (1) attributes of PHC services, including accessibility of primary healthcare services, consultation time, drug cost, continuity of care, referral system, opening hours, waiting time, and drug accessibility; (2) attributes of PHC doctors’ workforce, including doctors’ attitude, competence, and accessibility; (3) attributes of PHC facility infrastructure, including basic facilities, diagnostic facilities and department settings. It was identified that some attributes of PHC services had positive impacts on participants’ preferences for PHC institutions, while the same attributes of PHC doctors were the opposite. Conclusion: There are three major factors that contribute to patients’ preferences for PHC institutions in China. Policy interventions to improve doctors’ workforce and facility infrastructure of PHC institutions are needed to promote patients’ preferences for PHC.