The impact of groundwater recharge on nitrogen fixation efficiency (NFE) in arid groundwater-dependent ecosystems (GDEs) under climate change remains poorly understood. This study aims to reveal the changes in the driving role of groundwater recharge on the NFE of GDEs under different future climate change scenarios by integrating multi-feature datasets and combining the interpretable SHAP method and partial least squares structural equation modeling (PLS-SEM). Results indicate that both groundwater recharge and nitrogen fixation efficiency in ecosystems exhibit increasing trends under the SSP126 scenario, rising by 5.8% and 29.56%, respectively, and further increasing to 9.8% and 46.64% under the SSP585 scenario. SHAP analysis indicated that at the global level, evapotranspiration, leaf area index, and soil moisture content were the main contributing factors under the SSP126 scenario, while solar radiation and air temperature were the main contributors under the SSP585 scenario. In contrast, groundwater recharge contributed most significantly in arid regions under both scenarios (SSP126: 12.33%; SSP585: 8.25%). Further PLS-SEM analysis showed that in the historical period, groundwater recharge may have had a limiting effect on nitrogen fixation efficiency, specifically a direct negative impact of-0.16 from hydrology on NFE. However, under the SSP126 scenario, this limitation shifted to a promoting effect, with hydrology having a direct positive driving effect of 0.41 on NFE, with groundwater recharge dominating the loadings. Under the SSP585 scenario, this positive driving effect was weakened, with a direct impact of 0.16 from hydrology on NFE, but groundwater recharge still dominated the loadings. This discovery will have important implications for the study of GDEs and biodiversity conservation.