Heavy rains hit Shanxi in recent days, the country's biggest coal-producing province, after record floods struck the mining region of Henan in July.
Thermal coal on the Zhengzhou Commodity Exchange rose as much as 8 per cent on Tuesday, reports the BBC.
The floods further complicate China's efforts to increase fuel supplies to ease its deepening energy crisis.
Shanxi Province, which produced around a third of China's coal supplies this year, was forced to temporarily shut dozens of mines due to flooding. Although some sites are now slowly resuming operations.
At least 15 people have died during the severe flooding that has affected more than 1.76 million people in the province, local officials said on Tuesday.
Torrential rain last week led to houses collapsing and triggered landslides across more than 70 districts and cities in the northern province.
Even before the flooding, China was already facing an energy shortage which has caused power cuts in large parts of the country.
In recent weeks, energy firms have been forced to limit electricity supplies to millions of homes and businesses.
On Friday, Beijing reportedly ordered China's coal mines to boost output.
The move was the latest attempt by authorities to increase coal supplies after prices hit record highs and electricity shortages forced energy firms to ration power.
Since last month, a series of power cuts have forced factories to cut back production or stop operations completely
Manufacturing hubs in the northeast of China have been hit particularly hard.
The latest rise in the price of thermal coal prices comes on top of a 12 per cent jump on Monday.
Energy prices have been rising across the world as the global economy starts to emerge from the pandemic.
On Monday, the cost of Brent crude hit its highest since level October 2018, while US-traded oil touched a fresh seven-year-high.