Xi, who was greeted with a rare 21 salvos of artillery at the Prague Castle, the seat of the presidency, signed the document today together with his host, President Milos Zeman.
He said through a translator it "sets a political direction for the development of our relations in the future."
Xi's visit his only stopover in Europe before flying to the US is a result of a more business-oriented Czech approach to China than the one that prevailed under the late President Vaclav Havel, a prominent proponent of human rights.
He said business deals to be signed during Xi's visit could bring some 95 billion koruna ($3.9 billion) of Chinese investment this year. Details were expected to be announced tomorrow.
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Xi also backed a series of other deals on cooperation in health, transport, IT, sciences, tourism, banking and other fields as well a partnership deal between the countries' capitals.
He was scheduled to meet Prime Minister Bohuslav Sobotka, the speakers of both chambers of Parliament and Prague's mayor later Tuesday.
Several supporters of the Falun Gong group that has been banned in China were in the streets of Prague on Tuesday morning, while others waving Tibetan flags were gathering to protest the China's human rights record near a palace where Xi was meeting the Czech leaders.