As the affiliation network of churches may potentially benefit public health, the impact of participants’ preferences on the affiliation network bears further study. This paper attempts to use agent-based modeling techniques associated with geographic information to study the affiliation network between churches and participants. Using churches in ZIP Code 30318 in Atlanta in Georgia, this study specifies the preferences of participants as personal radii and choice patterns. Results suggest (1) personal radii of participants are positively related to the size of affiliation network and the centralities of churches; (2) the change of choice pattern of participants can lead to a sharp reduction in size of the affiliation network of churches; (3) The centralities of churches among the affiliation network are corresponding to population density of census tracts. Findings can be used to understand the formulation of affiliation network of churches and their relationship with participants’ preferences.