Xi said Lee, who was ethnically Chinese, was "widely respected by the international community as a strategist and a statesman" and expressed "sincere condolences" to his relatives.
"Lee is a strategist with both oriental values and international visions," Chinese Foreign Ministry spokesperson Hong Lei said in a statement.
Hong said that Lee was "a uniquely influential statesman in Asia" who made "historic contributions" to Singapore's ties with Beijing.
China expressed "deep condolences and sincere solicitude to the Singaporean government, its people and the relatives of Mr Lee Kuan Yew for his passing", Hong said.
Lee Kuan Yew, Singapore's founding father, served as the country's prime minister from 1959 to 1990 and then as a senior minister and minister mentor. He died early on Monday aged 91.
As a founder of China-Singapore relations, Lee had been committed to the promotion of mutually beneficial cooperation and made historical contribution for the establishment and development of bilateral ties, said Hong.

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