"We had a frank discussion about human rights, as we have in the past," Obama said, branding China's treatment of political dissidents and minorities "problematic".
The two delegations promised not to spy on each other's private enterprises for commercial gain, but here again, Obama used tough language, declaring: "I indicated it has to stop."
Xi protested that "China strongly opposes and combats the theft of commercial secrets and other kinds of hacking attacks".
The Chinese leader also firmly pushed back on human rights criticism, warning that reform would come on China's own timetable and without undermining its stability.
"We must recognise that countries have different historical processes and realities, that we need to respect people of all countries in the rights to choose their own path independently," he said.
There was also a sharp exchange over China's bid to extend its sovereignty over the South China Sea by building bases on reclaimed islands in areas disputed by Washington's southeast Asian allies.
"Islands in the South China Sea, since ancient times, are China's territory," Xi declared. "We have the right to uphold our own territorial sovereignty and lawful and legitimate maritime rights and interests."
Obama said the disputes must be settled in accordance with international statutes, noting the US was not a claimant.
Both countries signed a "joint vision" ahead of December's UN climate summit in Paris, and China committed to a domestic "cap and trade" carbon exchange. China will also set aside US$3.1 billion ($4.85 billion) to help developing countries fight climate change.
"If the world's two largest economies, energy consumers and carbon emitters come together like this, then there is no reason for other countries, whether developed or developing, to not do so as well," Obama said.
- AAP