Compared with direct radiation, diffuse radiation could be more efficiently used for photosynthesis because of the diffuse fertilization effect (DFE). Because carbon uptake and water loss are coupled through leaf stomata, DFE probably increases gross primary productivity (GPP) and evapotranspiration (ET) simultaneously. Multi-year eddy covariance flux observation data and simulated diffuse fraction of photosynthetically active radiation (PAR) for nine ecosystems across China (containing forest, grassland, wetland, and cropland) were used to quantify the impact of DFE on water use efficiency (WUE). The results showed that GPP firstly increased and then decreased with increasing diffuse fraction of PAR (kd-PAR = diffuse PAR/PAR) for each ecosystems. The kd-PAR values at which maximum GPP occurred varied between 0.34 and 0.76 across nine ecosystems. ET decreased with increasing kd-PAR in most ecosystems mainly because high kd-PAR (indicating low PAR) could reduce evaporation in most ecosystems. The relationships between WUE and kd-PAR were significantly linear with averaged slopes of forest, grassland, wetland, and cropland of 1.64, 0.96, 1.19, and 4.51 g C kg−1 H2O, respectively. A multiple linear regression method was used to analyze the effect of diffuse PAR (PARdif) and direct PAR (PARdir) on GPP and ET. The conversion efficiencies for PARdif were greater than for PARdir, and the relative differences were 178.35% and 23.77% for GPP and ET, respectively. The intensity of DFE for GPP and ET were greater for forest and cropland than for grassland and wetland. The intensity of DFE was 3.05 to 236.96 times higher for GPP than for ET. The mathematical analysis results demonstrated that the promoting effect of PARdif was greater for GPP than for ET, thereby inducing an increase in WUE with increasing kd-PAR. These results will be helpful for improving modeling accuracy of carbon and water cycles under the conditions accompanying global climate change.