In Zhengzhou, a city of over 12 million on the banks of the Yellow River, 12 people died in a flooded subway line while more than 500 were pulled to safety, the local government said.
Video on social media on Tuesday showed commuters chest-deep in murky floodwaters on a train in the dark and an underground station turned into a large, churning pool.
The rainfall has also resulted in the bursting of major river banks and flooding of streets in a dozen cities, upending daily lives of millions of people.
In Zhengzhou, the local flood control headquarters said the city's Guojiazui reservoir had been breached but there was no dam failure yet.
About 100,000 people in the city have been evacuated to safe zones.