Introduction Despite policy measure to strengthen and promote primary care, Chinese patients increasingly choose to access higher level hospitals. The resulting overcrowding at higher level hospitals and underutilisation of primary care are viewed to diminish the effects of the continuing health system investments on population health. We explore the factors that influence the choice of healthcare facility level in rural and urban China and aim to reveal the underlying choice processes. Methods We conducted eight semistructured focus group discussions among the general population and the chronically ill in a rural area in Chongqing and an urban area in Shanghai. Respondents’ discussions of (evidence-based) factors and how they influenced their facility choices were analysed using qualitative analysis techniques, from which we elicited choice process maps to capture the partial order in which the factors were considered in the choice process. results The factors considered, after initial illness perception, varied over four stages of health service utilisation: initial visit, diagnosis, treatment and treatment continuation. The factors considered per stage differed considerably between the rural and urban respondents, but less so between the general population and the chronically ill. Moreover, the rural respondents considered the township health centres as default and prefer to continue in primary care, yet access higher levels when necessary. Urban respondents chose higher levels by default and seldom moved down to primary care. Conclusions Disease severity, medical staff, transportation convenience, equipment and drug availability played important roles when choosing healthcare facilities in China. Strengthening primary care correspondingly may well be effective to increase primary care utilisation by the rural population but insufficient for the urban population. The developed four-stage process maps are general enough to serve as the basis for (partially) ordering factors influencing facility level choices in other contexts.