Integrated flood risk management based on urban policies remains challenging compared with infrastructure due to the unclear risk‐reduction effects over time. To consider heterogeneity in social responses to urban planning measures, a previous study developed an agent‐based household relocation model under flood risk (AHR‐FLOOD) by combining flood‐inundation and agent‐based relocation models. However, accurate modelling of relocation incentives remains challenging. This study aimed to improve AHR‐FLOOD by introducing spatial amenities based on transportation convenience and reflecting their impact on the decision‐making processes of agents to analyze the development of different flood risk areas. AHR‐FLOOD considering access to public transportation reproduced the spatial characteristics of the actual population and housing prices. The development of low‐risk areas reduced flood exposure and resulting flood damage. However, this effect was less clear for low‐income individuals, but the development of low‐amenity areas had the potential to induce low‐income population to move to safe areas. Chain migration was observed as a long‐term effect of the spatial amenity policy. This study presents insights into the effect of transportation policies on flood safety for long‐term spatial distance management in an agent‐based approach with the rigorous modelling and validation of local amenity impact on household relocation choices.