South Sudan's President Salva Kiir arrived Tuesday in Beijing to meet with Hu. Beijing is one of the main oil customers of South Sudan.
Hu said during his meeting with Kiir that he hoped the South Sudanese government would treat Sudan as an equal partner in peace.
"China sincerely hopes that South Sudan and Sudan will become good neighbors and partners that can live in harmony and realize common development," he was quoted by China's state-run news agency Xinhua as saying.
South Sudan announced last week that it was pulling its forces from Heglig, an oil town near ill-defined borders of the countries. Kiir told Hu that he was looking to ease tensions with Khartoum, Xinhua adds.
Sudanese President Omar al-Bashir, meanwhile, was quoted by the independent Sudan Tribune as saying he ordered his forces to "purge" Heglig of rebel forces.
A peace agreement signed in 2005 ended a Sudanese civil war, one of the bloodiest conflicts since World War II. South Sudan gained independence in July as part of that deal, though disputes over oil, border clashes and ethnic tensions threaten the peace.