Continuity of care can bring a wide range of benefits to consumers, providers and health care systems. This study aimed to understand the relationship preferences of primary care patients and their associations with patient experience of continuity of care.A questionnaire survey was conducted on 700 patients who sought medical care from a community health organisation in Beijing. The survey contained four items examining the relationship preferences of the respondents, and a modified Questionnaire of Continuity between Care Levels (CCAENA) measuring patient experience of continuity of care based on a three dimensional (relational, informational and managerial) model. The associations between the relationship preferences and the experience of respondents in continuity of care was tested using a linear regression model controlling for age, sex, education, medical insurance, personal income and servicing facilities.The respondents experienced relatively lower levels of informational and managerial continuity compared with relational continuity of care. More than 80% of respondents preferred free choice and a continuing relationship with doctors, compared with 59% who endorsed community facility control over hospital appointments. A preference for a continuing relationship with doctors was associated with all aspects of continuity of care. A preference in favour of community facility control over hospital appointments was a strong predictor of managerial continuity (β = 0.333, p < 0.001) and informational continuity (β = 0.256, p < 0.001). Patient preference for free choice of doctors was positively associated with relational continuity with specialists (p < 0.001), but not with primary care providers (p > 0.08). Perceived importance of information exchange was associated with relational and managerial continuity (p < 0.05), but not with informational continuity (p = 0.34).Patients prefer a high level of freedom of choice and sustained individual relationship with doctors. Relationship preferences of patients are associated with their experience of continuity of care. But patient strong preference for free choice of doctors is not aligned with relational continuity with primary care, a desirable feature of cost-effective healthcare systems.