He was the only candidate standing for the role of FAO Director-General, and received 168 out of 182 votes in a ballot in Rome on Sunday.
Qu, a former Chinese government minister who was nominated for the post by Beijing, will serve a new four-year term from August 1.
His appointment is seen as a part of a drive by Beijing to get more Chinese figures into senior jobs at international bodies.
Qu, a biologist by training, was vice-minister of agriculture before taking over as head of the UN agency in 2019.
FAO directors can hold the role for a maximum of two consecutive terms.
The vote came during the FAO Conference, which runs until July 7.
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