Vice Foreign Minister Zhang Yesui summoned Daniel Kritenbrink, US charge d'affaires in China, on Friday night, according to the Foreign Ministry's website.
"Nobody can shake the will and determination of the Chinese government and people to oppose outside interference and to safeguard the national sovereignty and unification," Zhang was quoted as saying by the official Xinhua news agency.
Beijing firmly opposes any foreign country allowing the Dalai Lama to visit, and objects to any foreign officials' meetings with him in any fashion, he said.
The meeting with Obama took place despite warnings from Beijing that it would "gravely sabotage China-US cooperation and relations, and will definitely undermine its own interests," Zhang said.
"The key to ensure the healthy and steady growth of China-US relations is to respect the other's core interests and major concerns."
Zhang demanded the US stop interfering in China's internal affairs, making use of Tibetan issues and "conniving and supporting anti-China secessionist activities" of the Dalai Lama and his followers.
"The United States must take concrete actions to regain the trust of the Chinese government and people," Zhang said.
Foreign Ministry spokesman Qin Gang said China has repeatedly expressed its serious concern over the monk's visit to the US.
"The Dalai Lama is a political exile who has long engaged in anti-China secessionist activities in the name of religion," he said.
The meeting with Obama was the first since July 2011, which also provoked protests from Beijing.
Obama emphasized that the US position is that "Tibet is part of the People's Republic of China," according to a statement issued after the meeting.
The Dalai Lama said he "hopes that dialogue between his representatives and the Chinese government will resume," the statement said.
A National Security Council spokesman said before the meeting that the US is "concerned about continuing tensions and the deteriorating
human rights situation in Tibetan areas of China." The Dalai Lama fled to India after China cracked down on a Tibetan uprising in March 1959. The 78-year-old spiritual leader is spending several weeks in the United States on a speaking tour.