Li, a senior economic and financial policy-maker in China, will take over from the incumbent Kandeh K Yumkella, whose second term ends in June.
The minister fought off competition from candidates of Afghanistan, Cambodia, Italy, Poland and Thailand to win the election, official media here reported.
A spokesperson for China's Foreign Ministry, Hua Chunying congratulated Li on his election.
"We are here to extend our congratulations to Li, while saying thanks to all countries for their support and trust," she told a media briefing.
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The newly elected head of UNIDO has also been a member of the monetary policy committee of the Chinese central bank for a decade.
"We believe Li is able to lead the UNIDO Secretariat to better serve all member states, while boosting sustainable development and international industrial development cooperation at the same time," she said.
UNIDO is a specialised agency of the United Nations that seeks to promote industrial development for poverty reduction, inclusive globalisation and environmental sustainability.