We studied the impacts of an increasingly common change in land use from paddy field to jasmine fields on the emission of greenhouse gases (GHGs), which have supposed the transformation of more than 1200 ha only in the last decade in the surroundings of Fuzhou city in response to economic changes. The possible increases that this can suppose constitutes and environmental concern in China. We studied areas dedicated to rice crop that have been partially converted to jasmine cultivation with some parts still kept as rice fields. Emissions of CO2, CH4 and N2O varied significantly among the seasons. CO2 and CH4 cumulative emissions and the global-warming potential (GWP) of these emissions were significantly lower in the jasmine than the paddy field. N2O emission, N2O cumulative emission, however, were higher in the jasmine than the paddy field, despite in some concrete studied periods the differences were not statistically significant. The total decrease in GHG emissions from the conversion from rice to jasmine production was strongly influenced by the indirect effects of various changes in soil conditions. The expected changes due to the great differences in water and fertilization use and management and organic matter input to soil between these two crops were in great part due to modified soil traits. According to structural equation models, the strong direct effects of the change from rice to Jasmine crop reducing the emissions of CO2 and N2O were partially decreased by the indirect effects of crop type change decreasing soil pH and soil [Fe2+] for CO2 emissions and by decreasing soil salinity and soil [Fe3+] for N2O emissions. The negative effects of the crop conversion on CH4 emissions were mostly due to the globally negative indirect effects on soil conditions, by decreases in soil salinity, water content and [Fe2+]. Soil salinity, water content, pH, [Fe2+], [Fe3+] and [total Fe] were significantly lower in the jasmine than the paddy field, but temperature had the opposite pattern. CO2 emissions were generally correlated positively with salinity, temperature, and water content and negatively with [Fe3+] and [total Fe] in both fields. CH4 emissions were positively correlated with salinity, temperature, water content and pH in both fields. N2O emissions were positively correlated with temperature and were negatively correlated with water content, pH, [Fe2+], [Fe3+] and [total Fe] in both fields. CO2 was the most important GHG for the GWPs, and the total GWP was significantly lower for the jasmine than for the rice cropland field. The change in the land use in this area of paddy fields will decreased the global GHG emission, and the effect on the GWPs was mostly due to changes in soil properties.