Abstract: Ecological compensation standard for marine reserve is the foundation of establishing the ecological compensation mechanism of marine reserve.According to the classification management of Xiamen Rare Marine Species National Nature Reserve, the marine area was divided into seven parts:West Port area, Tongan bay mouth, Jiulong estuary, Southwest area, East area, Tongan bay and Dadeng area.Taking the Chinese white dolphins (Sousa chinensis) as example, this paper estimated the contribution rate of different areas to the value of Xiamen marine reserve and the value per unit area by the expert investigation method.The damages of 10 types of human activities on the marine reserve were also estimated by the expert investigation method, which were marine reclamation land, harbor/anchorage, bridge construction, mining, ship repairing/shipbuilding, tourism/entertainment, submarine engineering, drain contamination, sea-route and construction.Thus the estimation model of ecological compensation standard was built and applied on the marine reclamation land in Xiamen Rare Marine Species National Nature Reserve to get the ecological compensation standards of Xiamen marine reserve in seven parts.This research filled the blank of the ecological compensation standard of the marine reserve at present.