The Yellow River Delta Wetland is one of the youngest wetlands, and also the most complete, extensive wetlands in China. The wetland in this delta is ecologically important due to their hydrologic attributes and their roles as ecotones between terrestrial and aquatic ecosystems. In the study, the spatial and temporal variation characteristics of CH4 and CO2 emission flux under five kinds of land use types in the wetland were investigated. The results indicated that the greenhouse gas emission flux, especially the CO2 and CH4, showed distinctly spatial and temporal variation under different land use types in the wetland. In the spring, the emission flux of CO2 was higher than that of CO2 in the autumn, and appeared negative in HW3 and HW4 in the autumn. CH4 emission flux of HW4 and HW5 was negative in the spring and autumn, which indicated that the CH4 emission process was net absorption. Among the five kinds of land use types, the CO2 emission flux of HW4 discharged the largest emission flux reaching 29.3 mg•m −2 •h −1 , but the CH4 emission flux of HW2 discharged the largest emission flux reaching 0.15 mg•m −2 •h −1 . From the estuary to the inland, the emission flux of CO2 was decreased at first and then appeared increasing trend, but the emission flux of CH4 was contrary to CO2.