Most evaluation systems don’t consider the problem of evaluation index selection, so the evaluation delay increases, and the evaluation results are not ideal, in order to solve the above problems effectively, a system to evaluate the water resources environmental carrying capacity in island tourism based on frequency analysis method is proposed and constructed. Through the study of the concept and connotation of water resources environmental carrying capacity in island tourism, combined with the system analysis theory, the principle of comprehensive evaluation indicator selection is established; the basic indicators are screened by frequency analysis method, and the evaluation system of water resources environmental carrying capacity in island tourism is established. According to the established system, a comprehensive evaluation model is set up to evaluate the environmental carrying capacity of water resources in island tourism. The simulation results show that the proposed system can effectively reduce the delay and improve the accuracy of the results to evaluate the environmental carrying capacity of water resources in island tourism.