Changes in the hydrological process caused by urbanization lead to frequent flooding in cities. For fast-growing urban areas, the impact of urbanization on the hydrological process needs to be systematically analyzed. This study takes Zhengzhou as an example to analyze the impact of urbanization on the hydrological process based on 1971–2012 hourly rainfall-runoff data, combining Geographic Information Systems with traditional hydrological methods. Our study indicates that the rain island effect in different districts of city became stronger with the increase of its built-up. The uneven land use resulted in the difference of runoff process. The flood peak lag was 25–30% earlier with the change of land use. The change of flood peak increased by 10–30% with the change of built-up. The runoff coefficient increases by 20–35% with the increase of built-up, and its change increased with the change of land use. Affected by the rain island effect, precipitation tends to occur in areas where built-up is dominant, which overall magnifies the impact of urbanization on the hydrological process. This provides new ideas for urban flood control. Refine flood control standards according to regional land use changes to cope with the hydrological process after urbanization.