Reverse osmosis (RO) and multiple-effect distillation (MED) are China's main seawater desalination technologies. This paper made the cost analysis of RO and MED industries, compiled China's 2007, 2012 and 2017 input-occupancy-output tables with RO and MED industries specially separated, then estimated their economic and environmental impacts in China's macroeconomic system. Results show that RO and MED had a similar pulling effect on China's economy, and their pulling effects were higher than the average level of all 50 industries. From 2007 to 2017, the ranking of direct CO2 emission coefficient of MED industry rose from 5th to 3rd, and that of RO industry rose from 12th to 8th. Expanding the unit output of the seawater desalination industry brought more CO2 emission than the average level of all industries. Unit production of MED brought more CO2 emission than that of RO. With the CO2 emission APL model, the upstream three energy production industries, which had the strongest connection with the CO2 emission of RO and MED industries were identified. To reduce CO2 emission from RO and MED industries, it is practical to take CO2 emission reduction measures on the upstream three energy production industries.