The marine ecosystem services consist of four elements such as provisioning service, regulating service, cultural service and supporting service. The regulating service value is one of the key constituents of marine ecosystem service values. There are corresponding evaluation indexes and methods for marine regulating service value in the current national standard ‘Technical directives for marine ecological capital assessment’ (GB/T 28058-2011), but it is not consistent with the evaluation system of terrestrial ecosystem. In order to better integrate the evaluation system of terrestrial ecosystem and bring the evaluation of marine ecosystem service values into the national economic accounting system, the evaluation indicators and methods of marine regulating service value were first improved in this paper, the application verification was carried out by taking Wenzhou coastal waters as an example, and the results were compared with those of the national standard method. Three indicators including carbon sequestrating, climate regulating and waste disposal are selected to evaluate the regulating service value provided by marine ecosystem in Wenzhou city from 2013 to 2017. The replacement-market-price method and the replacement-cost method are used to value these indicators. The spatial distribution map of the regulating service value in Wenzhou coastal waters are also preliminarily revealed. The results show that adopting the improved evaluation indicators and methods, the regulating service value in Wenzhou coastal waters is 63.59-86.25 billion yuan, in which the value of waste disposal service makes a major contribution about 56.53%-76.64% of the total regulating service and the climate regulating service is lower in value with about 23.33%-43.45%.of the total regulating service. The values of these two services account for more than 99.9% of the total regulating service value. According to the space range of 8649 km² in Wenzhou coastal waters, the average distribution density of regulating service value from 2013 to 2017 is valued as high as (73.52-99.72) ten thousand yuan/km². Additionally, the regulating service value provided by marine ecosystem in Wenzhou city is equivalent to 7.34%-11.88% of Wenzhou's marine gross products, and about 1.26%-2.00% of Wenzhou's gross domestic product (GDP) in the same year, and the contribution to the added value of secondary industry is 17%-27%. It is shown that the marine regulating service value has played an important supporting role in the economic development of Wenzhou city. The spatial distribution of the regulating service value in Wenzhou coastal waters shows an obvious decreasing trend from inshore to offshore. The use of new evaluation indicators and methods can greatly increase the marine regulating service value (about 6-9 times), compared with that of the old evaluation system, thus the total marine ecosystem service values in Wenzhou city are greatly increased. The evaluation of the regulating service value provided by ecosystem in Wenzhou coastal waters from 2013 to 2017 can reflect the good state of marine ecological environment in Wenzhou city in recent years, and show that marine ecosystem has brought great benefits to human beings. It can also provide a certain decision-making basis for the construction of marine ecological civilization and the management of marine administrative departments at the present stage.