Abstract: A distributed hydrological model was developed by integrating and improving the modified SWAT2000 to take quantitative research on water transformation of rice-based irrigation system in hilly area of south China. Thinking over the hydrological process and the special characteristics of rice-based irrigation system in hilly area, the main ameliorations, including the simulation framework, the factors of water balance (rainfall, ET (evportranspirtion), seepage, irrigation and drainage) and the canal seepage influence, could further improve the efficiency of simulation. Then the new modified SWAT was validated in a representative small watershed in Zhanghe Irrigation System and the simulation results were compared with the results of the original SWAT. The index of simulation efficiency, including the relative error (RE), linear regression coefficient (R2) and the Nash-Suttclife simulation efficiency coefficient (Ens), were used to the simulation results evaluation. The RE of the total runoff was within ±10.0% for the simulation values of the new modified SWAT and the observed values, but it took only 30% to 40% of the observed total runoff for the original SWAT. The R2 of the daily runoff were larger than 0.85 for the simulation values of the new modified SWAT and the observed values, while they varied from 0.76 to 0.91 for the simulation values of the original SWAT and the observed values. The Ens of the daily runoff ranged from 0.57 to 0.74 for the simulation values of the new modified SWAT and the observed values, while they were lower than 0.50 for the simulation values of the original SWAT and the observed values, even just was negative. The RE of the rice ET was only ?4.76% for the simulation values of new modified SWAT and the observed values, but it reached to -38.49% for the original SWAT and the observed values. The R2 of the rice ET reached to 0.93 for the simulation values of the new modified SWAT and the observed, while it just was 0.73 for the original SWAT and the observed values. The Ens of the rice ET was up to 0.85 for the simulation values of the new modified SWAT and observed, but it was negative for the original SWAT and the observed. The results suggested that the new modified SWAT was more effective and suited than the original SWAT. It can be a good way to study water transformation and water saving potential in rice-based irrigation system.