BackgroundAlthough primary health care (PHC) has been proven to be effective in preventing and treating chronic diseases, the visits rate of PHC institutions is still not ideal. Some patients initially express a willingness to visit PHC institutions but end up seeking health services at non-PHC institutions, and the reasons for this behavior remain unclear. Therefore, the objective of this study is to analyze the factors that contribute to behavioral deviations among chronic disease patients who originally intended to visit PHC institutions.MethodsData were collected from a cross-sectional survey among chronic disease patients with original intention to visit PHC institutions in Fuqing City, China. The analysis framework was guided by Andersen’s behavioral model. Logistic regression models were employed to analyze the factors affecting the behavioral deviations among chronic disease patients with a willingness to visit PHC institutions.ResultsA total of 1,048 individuals were finally included and about 40% of the participants with the original willingness to seek care from PHC institutions finally chose non-PHC institutions in their subsequent visits. The results of logistic regression analyses indicated that at the predisposition factor level, older participants (aOR60-69= 0.602,P< 0.01; aOR70-75= 0.475,P< 0.01) were less likely to have behavioral deviations. At the enabling factor level, compared to those covered by Urban Employee Basic Medical Insurance (UEBMI) and not reimbursed, those covered by Urban–Rural Resident Basic Medical Insurance (URRBMI) (aOR = 0.297,P< 0.01), and those answering that reimbursement from medical institutions was convenient (aOR = 0.501,P< 0.01) or very convenient (aOR = 0.358,P< 0.001) were less likely to have behavioral deviations. At the need factor level, participants who visited PHC institutions due to illness last year (aOR = 0.348,P< 0.001) and with polypharmacy (aOR = 0.546,P< 0.01) were less likely to have behavioral deviations compared to those without the visit of PHC institutions and not taking polypharmacy, respectively.ConclusionsThe deviations between the original willingness of PHC institution visits and subsequent behavior among chronic disease patients were associated with a number of predisposing, enabling, and need factors. Developing the health insurance system, strengthening the technical capacity of PHC institutions, and steadily developing a new concept of orderly healthcare-seeking behavior among chronic disease patients, will help promote their access to PHC institutions as well as improve the effectiveness of the tiered medical system for chronic disease care.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12913-023-09528-y.