Doksuri smashed into southern Fujian province on Friday morning with gusts of up to 175 kilometres per hour (110 miles per hour), and China's meteorological service said Saturday its "influence" was now being felt in the country's north.
China has been experiencing extreme weather conditions and posting record temperatures this summer, events that scientists say are being exacerbated by climate change.
Experts have warned Saturday's downpour could prompt even worse flooding than in July 2012, when 79 people died and tens of thousands were evacuated, according to local media.
It is the first time since 2011 that such a heavy rainfall warning has been issued, local media said.
The red alert will be in force from 8 pm local time (1200 GMT), and covers an area of several hundred million inhabitants, including the metropolis of Tianjin, and the provinces of Hebei and Shandong.
Several of Beijing's parks, lakes and riverside roads have been closed out of precaution, the municipal authorities announced on Saturday.
Heavy showers were reported in the capital on Saturday afternoon and are expected to last through Tuesday.
In Fujian's provincial capital on Saturday authorities ordered residents to only leave their homes only if necessary.
Public transport has also been suspended.
Doksuri had been a super typhoon as it tore across the Pacific Ocean earlier this week, but lost some intensity as it neared the Philippines.
The typhoon killed at least 13 people there, and caused landslides and floods before tracking northwest to China and gradually weakening.
It still brought colossal waves and howling winds to the country's southeast on Friday, causing significant damage.
In Xiamen, a major port city on the Taiwan Strait, heavy weather appeared to have ripped the roof off of a bus station and pushed it up against a nearby sign.
Some streets in the city were strewn with fallen trees, while significant flooding elsewhere impeded passage by vehicles and brought police to the scene.
Pictures shared on social media showed massive gusts of wind pummelling residential tower blocks on Friday in Jinjiang, a county-level urban area south of the city of Quanzhou.
Videos of huge waves crashing over embankments and fierce winds whipping through urban areas were posted to the social media platform Weibo by the state-backed People's Daily.
The stormy weather follows weeks of record heat in China.
At the beginning of July, Beijing and the surrounding region broke temperature records, with local temperatures in excess of 40 degrees Celsius (104 Fahrenheit).
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