Abstract Background In China, integrated care is facilitated by interdisciplinary Family Physician Teams (FPTs) to extend primary care services without increasing physician numbers. However, the advancement of integrated care faces challenges due to insufficient motivators for Family Physician Team Members (FPTMs). Objective To elucidate the motivational preferences of FPTMs within integrated care, highlighting preference heterogeneity across individuals with diverse demographic and professional characteristics. Methods A cross-sectional study was conducted in November 2022 with 363 FPTMs at community health centers affiliated with seven hospitals in Shenzhen city. The study assessed motivational preferences using a best–worst scaling (BWS) questionnaire to collect data. Conditional logit and mixed logit models were employed to analyze overall preferences and heterogeneity. Results The study revealed a strong preference for patient-centered motivators, particularly highlighting patient needs, trust level, and adherence as key motivators that are crucial in shaping the engagement of FPTMs with integrated care. Additionally, heterogeneity in preference patterns was observed based on sex, education level, and professional role. Specifically, male FPTMs, those with a master’s degree or higher, and general practitioners demonstrated a significantly stronger preference for employment benefits and government resource allocation. Conclusion The findings highlight the preference of FPTMs for patient-level motivators, underscoring the importance of implementing a feedback mechanism to capture patients’ perspectives on services. Policymakers are urged to develop tailored motivational structures that consider the varied preferences of team members across different roles, thereby motivating the provision of integrated care by FPTMs.