Since the early 1960s, especially after the publication of Costanza’s famous article in Nature in 1997, evaluation of ecosystem services has been one of the hottest and most debated issues in the field of ecology and ecological economics. Different opinions were expressed regarding the necessity and validity of evaluation using economic methods. The main difficulties for economic evaluation were discussed. Firstly, the complexity of ecosystem, including interdependence and transition of spatial-temporal scaling of various ecological functions lead to repeated calculation and difficult in extrapolating evaluation results. Secondly, the economic methods have their own limitation and weakness. For instance, different methods have been chosen in accordance with evaluation objects and purposes, and evaluation results rely very much on the methods selected.These cause non-comparability between the results. Lastly, economic methods could not always reflect real values of natural ecosystems when preferences of human to ecosystem services change with time and appearance of new information. It is recommended that future studies should focus on the above issues so as to ensure an objective and reliable assessment result, and provide a strong support for establishing ecological compensation mechanisms and improving ecosystem management.