The coastal zone is a dense human activity area, and has been under the heavy pressure from large population centers and various human activities. The scarcity and the use conflicts of coastal resources have become increasingly prominent problems. Coastal principal function zoning is an effective approach to solving these problems, and a helpful way to optimize resources allocation and support sustainable development. Determining the principal function is a key step in coastal principal function zoning. In this paper we make an attempt to apply economic analysis to the principal function selection in the coastal area of Xiamen Bay. Based on the distribution and characteristics of coastal resources, and the opinion of local residents revealed by a questionnaire investigation, we set two scenarios as alternative principal functions, i.e. to develop coastal tourism as a priority or to fully develop commercial port transportation in the research area. The net benefits of Scenario 1 and 2 are calculated by the constructed formulas, and the results are 3.4×1010 RMB Yuan/a and 7.4×109 RMB Yuan/a, respectively. Based on the economic analysis, we propose that coastal tourism should be chosen as the principal function in the coastal area of Xiamen Bay.