Mangrove reserves promote the protection of mangroves, but they also lead to the restriction of land development rights in the region, which is unfair to society. This paper aims to evaluate the impact of the spillover of coastal development. Taking the Shankou Mangrove Ecological Reserve in the Beibu Gulf of Guangxi as an example, this paper conducts a research design using the choice experiment. Conditional logit and a structural equation model are used to analyze data and to calculate the respondents' choice preferences and willingness to pay for the limited right to develop the coastal zone. Also, to reveal preference heterogeneity, individual characteristic factor analysis is added. The results show that: after the establishment of the protected area, regional differences are evident in the limited space of coastal development rights. Among them, the limitation degree of sea area use is the highest, followed by beach area; the degree of limitation on land area use is the lowest. The limited spatial differences of coastal development rights may lead to an imbalance in the development of coastal land resources among regions. Other problems include the forced idleness of coastal land resources and the threat to the livelihood of residents. Overall, this is not conducive to the coordinated development of an ecological economy in the reserve. This study can provide a decision-making basis for optimizing the coastal development rights management of coastal zone ecological protection areas. A reference for the coastal development rights management in other countries is also provided. •Coastal farmers’ dependence on land use is different from that of mainland farmers.•The externality of ecological protection policies decreases from coastal to inland.•Differences exist in preferences for land, tidal flat and sea development rights.•Land resource development in coastal zones is unbalanced between sea and land.