They met in Beijing's Great Hall of the People and spoke of the importance of positive ties between the two nations.
Mr Xi said he hoped her visit would build "mutual understanding". Ms Suu Kyi said her NLD party values Myanmar's friendship with China, Xinhua reports.
China was a close ally of Myanmar when it was under a military junta.
But since the end of military rule and the release of Aung San Suu Kyi from years of house arrest, the military-backed government of President Thein Sein has allied itself more closely with the US.
Correspondents say China is keen to build its relationship with the NLD (National League for Democracy), as it is expected to poll well in general elections in November.
Aung San Suu Kyi, however, is barred by the constitution from running for the presidency because her children are foreign citizens.
A long-awaited bill to amend the constitution was tabled in parliament on Wednesday, but retained the clause.
The bill also slightly reduces the role of the military, but allows it to keep a quarter of all seats in parliament.
The visit comes at a time of tensions between Myanmar and China, partly because of violence near their mutual border.
Myanmar has been fighting rebels in its eastern Kokang region, which borders China's Yunnan province.
China is concerned by instances of the violence spilling over its border. It has sent patrols to the border in response and recently carried out live fire drills in the region.
But on Thursday, the Kokang rebels announced a unilateral ceasefire, saying they wanted to take part in the general election.
The BBC's Jonah Fisher in Myanmar says the ethnically Chinese armed group released a statement saying they had taken the decision under pressure from the authorities in Beijing, but retained their right to self defence.
Myanmar's opposition leader Aung San Suu Kyi has met Chinese President Xi Jinping on the second day of her visit to China, state media report.