Freshwater ecosystems, as active components in global biogeochemical cycles, are known to be important sources of atmospheric greenhouse gases (GHGs). The quantification of GHGs budget from freshwaters has been subject to intensive research in recent years, while current assessments still exist enormous uncertainties due to their strong spatial and temporal heterogeneity. Particularly, uncertainties relating to methodology of monitoring GHGs fluxes in freshwater ecosystems might further constraint the accurate assessment for total contributions of freshwater ecosystems to global GHGs inventory. Previous reports used different methods for GHGs fluxes measurement can also strongly restrict the comparisons between global or regional freshwater ecosystem fluxes. However, previous studies have rarely focused on the systematic summarization of theory, algorithm and influencing factors of different monitoring methods for GHGs fluxes in freshwaters. This study summarized the general characteristics of GHGs emissions from freshwater ecosystems, and then sketched the basic theory, general algorithms and models of different GHGs fluxes monitoring methods, including floating chamber method, boundary layer model based method, micrometeorology method, and bubble traps method, which have been commonly used in freshwater ecosystems. We further analyzed the application environment and advantages and disadvantages of each method, respectively. Meanwhile, the main influencing factors being related to observation accuracy of floating chamber method and boundary layer model-based method were reviewed in detail. We highlighted that there were many inconsistent programs of chamber size, installation, sampling interval for floating chamber method, would influence the monitoring results. Uniform criterion and standard for floating chamber method and boundary layer model-based method should been developed in different aquatic environment. Furthermore, the comparative studies of the different monitoring methods were integrated. The results showed generally overestimated GHGs fluxes using the floating chamber methods compared with those deriving from the boundary layer model-based method. Moreover, the consistency between the observations using micrometeorological method and floating chamber method were still controversial. Our study suggests that the effect of the monitoring methods on the GHGs fluxes in freshwaters and their deviation source is an important challenge. Comprehensive assessment and comparison of various methods can improve the accuracy of GHGs measurement in freshwater ecosystems. Methodology of GHG fluxes measurement should be given priority attention in the further studies.