Abstract: To distinguish sea area use fee and ecosystem damage cost is the premise of making sea area resource price embody ecosystem damage reasonably. By analyzing the connotation of sea area use fee and ecosystem damage cost, the composition of cost, evaluation index and scope are compared simultaneously, which indicates there is intersection between the two. Natural attribute change fee included in sea area use fee belongs to ecosystem damage cost, but it is not enough to embody the entire ecosystem damage. The frequently mentioned marine ecological compensation fee is equal to ecosystem damage cost. Marine organisms compensation fee and pollutant discharge fee, which have been levied for a long time, are part of ecosystem damage cost. The natural attribute charge fee overlaps with the marine organisms compensation fee to some extent, while interlinks with the pollutant discharge fee without intersection. In order to determine the sea area price scientifically, it is proposed to enrich natural attribute change fee, merge marine organisms compensation, and draw a dividing line between natural attribute change fee and pollutant discharge fee.