Their talks came as Iran's top nuclear official, Saeed Jalili, was in China for talks.
Beijing agreed that sanctions were "not effective", Mr Jalili said.
"In our talks with China it was agreed that tools such as sanctions have lost their effectiveness,"
International sanctions would not prevent Iran from pursuing its nuclear activities, he told reporters in Beijing.
Chinese officials have not commented after the talks.
China's foreign minister has said he still hopes the nuclear issue can be resolved through negotiations.
Serious talks
China's President Hu called for "healthy and stable" relations with the US during the telephone call with Mr Obama.
The two leaders also discussed Taiwan and the importance of implementing G20 agreements to boost economic growth.
The exchange capped a week of easing tensions between the two big powers who have recently had high-profile disagreements over Tibet, trade and Taiwan.
But in the brewing confrontation between the west and Iran over its nuclear programme, China is now key to what happens next, says a local news channel, in Beijing.
Earlier this week President Obama said he wanted to see new UN sanctions on Iran "within weeks".
China, a veto-wielding UN Security Council member with strong ties to Iran, has in the past expressed reluctance to see new sanctions imposed.
However the US ambassador to the UN, Susan Rice, said on Thursday that China had indicated it was ready to hold "serious" talks with Western powers on a new UN resolution.
Western powers claim Iran seeks nuclear weapons, a charge Tehran denies.
Strained ties
The US and China have disagreed recently over Tibet and Taiwan.
Mr Hu warned Mr Obama not to antagonise Beijing on the issues, China's foreign ministry said.
"Hu stressed the Taiwan and Tibet issues concern China's sovereignty, territorial integrity, and China's core interests, and properly dealing with these issues is key to ensuring the healthy and stable development of Sino-US relations," said a ministry statement.
China was upset when Mr Obama met Tibet's spiritual leader, the Dalai Lama, in February. It was also angered by Taiwan securing a weapons deal from the US.
The US has supported the internet search company Google in its concerns over censorship in China, and other trade rows persist.
However, Beijing did allow the visit of the aircraft carrier USS Nimitz to Hong Kong in February.
One issue where China and US are in agreement is the need to bring North Korea back to the negotiating table over plans to end its nuclear programmes.
