A Geographic Information System (GIS) based conjunctive simulation model incorporating soil water, heat, nitrogen behaviors and crop growth was established and validated. The regional distribution of Water Use Efficiency (WUE) and Nitrogen Use Efficiency (NUE), and nitrogen loss were analyzed under summer maize-winter wheat rotation system, by estimation of the GIS-based model under the soil, meteorological and rural socio-economical condition in the Huang-Huai-Hai Plain of China (HHHP) from 1999 to 2000. Due to the variations in biophysical conditions and farming practices, the inter-physiognomy variations on WUE, NUE, as well as soil nitrogen leaching showed significant differences. The total soil nitrogen leaching of whole maize-wheat season in HHHP was 1.559x10⁹ kg, equaled to 15.12% of the total nitrogen fertilizer applied (NFA). The WUE in winter wheat season and summer maize season ranged from 0.65 to 1.56 kg·m^-3 (median 1.03 kg·m^-3) and from 0.67 to 1.60 kg·m^-3 (median 1.09 kg·m^-3) separately. The NUE in winter wheat season and summer maize season ranged from 9.60 to 32.70 kg·kg^-1 (median 18.42 kg·kg^-1) and from 14.31 to 37.90 kg·kg^-1 (median 20.02 kg·kg^-1) separately. In summer maize season, the multivariate stepwise regression results indicated that, nitrogen leaching was significantly positively correlated with NFA, saturated hydraulic conductivity (Ks), active accumulated temperature (ACT), rainfall and irrigation amount (RIA); WUE was significantly positively correlated with NFA and significantly negatively correlated with ACT; NUE was significantly positively correlated with RIA and significantly negatively correlated with NFA and soil organic matter (SOM). In winter wheat season, nitrogen leaching was significantly positively correlated with NFA, Ks and RIA; WUE was significantly positively correlated with NFA and sunshine hours (SH) and significantly negatively correlated with RIA and Ks; NUE was significantly positively correlated with RIA and SH and significantly negatively correlated with NFA and Ks. Acknowledgement:This research was supported by the national natural science foundation of China (40201023), and the Program for Changjiang Scholars and Innovative Research Team in University (IRT0412).