The alternative cost method and opportunity cost method were used to evaluate the value of ecological services provided by seaweed aquaculture based on the study of seaweed farming in Zhejiang Province and Jiangsu Province from 2005 to 2014. The results showed that the value of direct ecological services mainly included three factors: the value of carbon capture, the value of eutrophication regulation and the value of heavy metal removal. The value of indirect ecological services included the value of avoided transformed forest land, avoided use of water resources, avoided use of fertilizer and avoided use of pesticide. In 2014, the values of three seaweed aquaculture direct ecological services are 0.41 million RMB, 1.97 million RMB, 0.61 million RMB for Zhejiang Province and 0.26 million RMB, 1.24 million RMB and 0.38 million RMB for Jiangsu Province, respectively; the value of four indirect ecological services are 464.87 million RMB, 11.61 million RMB, 3.09 million RMB and 11.77 million RMB for Zhejiang Province and 293.22 million RMB, 7.32 million RMB, 1.95 million RMB and 7.42 million RMB for Jiangsu Province. The total value of ecological services of seaweed aquaculture is far greater than the direct economic value of seaweed. The vast area of coastline indicates that seaweed farming has great potential for development, and the promotion of seaweed farming can not only be a solution to address the arable land and food crisis, but also has a positive effect on reducing carbon emissions, reducing nutrient pollution and coping with global changes.