The uncle, Jang song-thaek, is seen as a driving force for reforms which the isolated and destitute North is believed to be trying and for which it desperately needs Chinese backing.
"For many years, Comrade Jang Song-thaek has done a great deal of work to develop neighbourly friendship between China and North Korea," Hu said at their meeting, according to Chinese radio.
Hu also offered condolences for floods that recently hit the North, which routinely struggles to feed its 24 million people.
"I'm confident that under the leadership of the Korean Workers' Party with Kim Jong-un as its First Secretary, the North Korean people will be able to overcome this flood disaster and build a beautiful homeland."
Jang's trip to China this week has been seen as the latest sign that Kim is seriously exploring ways to revive his reclusive country's economy, which has been in decline for years.
Jang attended meetings to discuss joint economic projects in Rason on the North's east coast, and in Hwanggumphyong, an area on the border between the two countries.
North Korea already relies heavily on China to support its economy, which has been dragged down by decades of mismanagement and international sanctions over its weapons programmes.
Kim's father, who died last December, flirted with reform but never really let it take root, wary of anything that might undermine his family's iron grip over the state.
But the new leader has presented a different image to his father and is believed to want economic and agricultural reform.
So far, North Korea has received little more than $300 million in non-financial direct investment from about 100 Chinese companies mainly in the food, medicine, electronics, mining, light industry, chemicals and textile sectors.
