The objective of this study is to quantify the values of greenhouse gases (GHGs) exchange in carbon equivalents of marshes and paddy fields in the Sanjiang Plain, Heilongjiang Province, China. We obtained the GHGs exchange values based on comparable price by calculating the carbon sequestration values and the GHGs emission values of marshes and paddy fields respectively in four periods of 1982, 1995, 2000 and 2005. It is noted that the GHGs emission values are always negative. In this study, the marshes areas decreased from 1438977.0 to 775,132.2ha and the paddy fields areas increased from 417195.8 to 934205.0ha. The values of GHGs exchange of marshes varied from 135877.156×106 to 136882.534×106 yuan (RMB) and those of paddy fields varied from 1006.256×106 to 2767.645×106 yuan. The GHGs exchange values of marshes decreased from 1982 to 2005 on the whole, reversely, those of paddy fields increased, but those in 2005 were lower than those in 2000. In different periods, the GHGs exchange values were always higher in marshes than in paddy fields. The contribution rate of GHGs exchange values per unit area of marshes was also very high in different periods, and the maximum was up to 98.35% in 2005. As far as the whole wetland ecosystem (including marshes and paddy fields), assuming a linear change in GHGs exchange values, it represented a cumulative increase of 20926.757×106 yuan from 1982 to 2005. By adding GHGs exchange values increased during those four periods, we obtained a cumulative net increase values of GHGs exchange of wetland ecosystem of 18200.860×106 yuan. The results will be useful for understanding the indirect services provided by marshes and paddy fields.