The degradation of ecosystems and their services is threatening human wellbeing, making ecosystem service (ES) conservation an urgent necessity. In ES conservation planning, conservation area identification is crucial for the success of conservation initiatives. However, different decision-making preferences have not been fully considered and integrated in ES conservation area identification. This study takes the Dawen River watershed as the study area and considers three water-related ESs to be conserved. We aim to integrate the decision-making preferences of cost-effectiveness, ES sustainable supply, and ES social benefit into identifying ES conservation areas by using conservation cost, ecosystem health, and ES social importance as spatial constraints, respectively. We identified ES conservation area alternatives under the scenarios set according to different decision-making preferences. Specifically, ES conservation targets, i.e., the expected proportion of each ES in conservation areas, are designed to be met where there is low conservation cost (cost-oriented scenario), high ecosystem health (ES sustainable supply scenario), or high ES social importance (ES social benefit scenario). A balanced scenario considering all three decision-making preferences together is further established. The results show that under each scenario, the identified conservation areas can concurrently meet the conservation targets and decision-making preferences. The consideration of different decision-making preferences can greatly influence the spatial distributions of ES conservation areas. Moreover, a severe trade-off between conservation cost and ES social importance is observed under the ES social benefit scenario, and the balanced scenario can achieve a synergy of decision-making preferences. Our study provides a method to integrate the decision-making preference into ES conservation area identification, which can improve the rationality and practicality of ES conservation planning.