To describe how patients choose between primary care institutions (PCIs) and non-PCIs using rational choice theory from the perspective of survival rationality, economic rationality, and social rationality. Multi-stage stratified sampling and convenience sampling were applied to select 1723 patients to conduct the questionnaire survey. Chi-square test and binary logistic regression were performed to analyze the factors associated with patients' choice of PCIs. In total 55.83% of 1723 patients would attend a PCIs for healthcare. The results of the univariate analysis revealed that patients who are female (58.46%, P = .015), suffering from chronic diseases (56.26%, P = .047), inpatients (67.58%, P < .001), Beijing (59.62%, P = .002), partial understanding of the family doctor contracting system (62.30%, P < .001), and not understanding of the medical alliance policy (58.04%, P = .031) had significantly higher probability of choosing PCIs. Logistic regression analysis showed that females were more unwilling to attend PCIs (odds ratio (OR) = 0.822, 95%CI: 0.676-0.999). Following survival rationality, patients without chronic diseases were more likely to attend PCIs (OR = 1.834, 95%CI: 1.029-3.268), and inpatients were more unlikely to attend PCIs (OR = 0.581, 95%CI: 0.437-0.774). From an economic rationality perspective, patients from the Fujian province were more likely to attend PCIs (OR = 1.424, 95%CI: 1.081-1.876). From a social rationality perspective, patients who partial understanding of the family doctor contracting system were more unlikely to attend PCIs (OR = 0.701, 95%CI: 0.551-0.892), and patients who partial and complete understanding of the medical alliance policy were more likely to attend PCIs (OR = 1.340, 95%CI: 1.064-1.687; OR = 1.485, 95%CI: 1.086-2.030). Survival, economic, and social rationality are involved in patients' choice to attend PCIs. Compared to survival rationality and social rationality, economic rationality showed a lower association with patients' choice to attend PCIs. Medical institutions are recommended to adopt a "patient health-centered" approach when providing medical services and further optimize the family doctor contracting system and construction of medical alliances.