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After his return, Zhu became professor first in Wuchang Higher Normal School and then in Nanjing Higher Normal School. In 1921 when Nanjing University set up the Department of Geography, he became its Dean. In 1927 when the Central Academy was established, he took the post of Director of the Meteorology Research Institute. In 1936 he became President of Zhejiang University.
In 1949, Zhu Kezhen became Vice President of the Chinese Academy of Sciences. Thereafter, he also served variously as vice chairman of the Chinese Association for Science and Technology, President of the Chinese Geographical Society, President of the Chinese Meteorological Society, Director of the Department of Bioscience and Geoscience, Chairman of the Integrated Investigation Committee of Natural Resources, Chairman of the Translation and Publication Committee, Chairman of the Committee for the History of Natural Science, etc. He was also member of the Standing Committee of the First National People's Congress.
He pursued science and democracy his entire life, making ground-breaking contributions in the fields of typhoon and monsoon meteorological research, climatology, phenology, natural divisions study, natural resources integrated investigation, and the history of science. His major works include An Outline of Meteorology in China, Phenology and The Inter-relationship between Meteorology and Agriculture as well as Selected Works of Zhu Kezhen.