In recent years, the combined effects of rapid urbanization and climate change have led to frequent floods in urban areas. Rainstorm flood risk warning systems play a crucial role in urban flood prevention and mitigation. However, there has been limited research in China on nationwide urban flood risk warning systems based on rainfall predictions. This study constructs a two-level early warning system (EWS) at the national and urban levels using a two-dimensional hydrological–hydrodynamic model considering infiltration and urban drainage standards. A methodology for urban rainstorm flood risk warnings is proposed, leveraging short-term and high-resolution rainfall forecast data to provide flood risk warnings for 231 cities in central and eastern China. Taking Beijing as an example, a refined rainstorm flood warning technique targeting city, district, and street scales is developed. We validated the methodology with monitoring data from the “7.31” rainstorm event in 2023 in Beijing, demonstrating its applicability. It is expected that the findings of this study will serve as a valuable reference for the urban rainstorm flood risk warning system in China.