It is critical for urban and regional planners to examine spatial relationships and interactions between a port and its surrounding urban areas within a region’s spatial structure. This paper seeks to develop a targeted framework of causal relationships influencing the spatial structure changes in the Bushehr port-city. Hence, the study utilizes Fuzzy Cognitive Maps (FCMs), a computational technique adept at analyzing complex decision-making processes. FCMs are employed to identify concepts that act as drivers or barriers in the spatial structure changes of Bushehr port-city, thereby elucidating the causal relationships within this context. Additionally, the study evaluates these concepts’ relative significance and interrelationships. Data was collected through interviews with ten experts from diverse backgrounds, including specialists, academics, policymakers, and urban managers. The insights from these experts were analyzed using FCMapper and Pajek software to construct a collective FCM, which depicts the influential and affected concepts within the system. The resulting collective FCM consists of 16 concepts, representing the varied perspectives and expertise of the participants. Among these, the concepts of management and planning reform, economic growth of the city-port, and port development emerged as the three most central concepts. Moreover, the effects of all influential concepts on the spatial structure change in Bushehr port-city were evaluated through simulations conducted across four different scenarios. The analysis demonstrated that the system experiences the most significant impact under the fourth scenario, where the most substantial changes are observed in commercial and industrial growth and the planning of port-city separation policies.