There is an increasing need for coastal and marine ecosystems conservation. However, information to guide management decisions for coastal and marine ecosystems is still lacking. Considering the present advantages and limitations of existing ecosystem services valuation (ESV) accounting methods, this paper proposes a detailed donor-side accounting approach, based on emergy method, which could be used as the basis for better policies-making on coastal and marine conservation. In particular, this includes a classification of different ecosystems, a system for ecosystem services (ES) classification, ES formation mechanism, as well as accounting techniques. The ES classification system includes direct, indirect and existence services. Accounting techniques presented here can overcome common limitations in existing accounting methods: (1) double counting; (2) evaluation from the receiver perspective; (3) the inappropriate use and replacement of unit emergy value (UEV). The present method is applied to the evaluation of coastal and marine ecosystems in the Pearl River Delta (PRD), China. Results show that (1) the total coastal ESV decreased from 2000 to 2009 in the PRD area, among which water purification contributes most to the decrease, followed by soil building, climate regulation and microclimate regulation; (2) the coastal ecosystems have the largest potential to regulate climate whether at micro or macro scale; (3) the marine ESV decreased with the ratio of 42.37%, and biomass increase and carbon sequestration account for the decrease; (4) intertidal marshes has the largest ESV per unit area, followed by mangrove, coral reefs and rocky marine shores, while the marine ecosystem has the smallest ESV per unit area. As proved by the case study, this work can provide a basis for an accounting method for coastal and marine ESV assessment, which could serve to improve both the management decision making processes and policy indications through accurately valuing coastal and marine ES, leading to additional investment in conservation of these ecosystems.