In this position he was pivotal in improving the field of history in Mongolia, by compiling archives, initiating scientific journals, and supervising the protection and research of important cultural sites.

His 1943 biography of Damdin Sükhbaatar established his reputation at home and abroad, but thereafter he primarily wrote on early modern topics, especially Qing-era Mongolia and the struggle for Mongolian independence.

He established archives of original historical documents and made a number available for public consumption at the National Library of Mongolia, while also helping to initiate journals on history, ethnography, and archaeology, and while supervising the research, protection, and restoration of cultural sites such as the Erdene Zuu monastery near Karakorum.

[3][8] Natsagdorj's international colleague Igor de Rachewiltz noted that he risked the ire of the communist government, who appointed him a State Great Khural deputy in the 1951 election, by not sticking to official positions on historical events.

[9] Natsagdorj substantially neutralised the overt bias and subtly contradicted the arguments of prominent Soviet scholar Ilya Petruchevsky, who had written the same chapters of the first edition.

The MPR's leader Yumjaagiin Tsedenbal took the chance to purge those behind what the Soviet Union immediately condemned as "Mongolian nationalism", including his main rival Daramyn Tömör-Ochir.

[11] A year after the Mongolian Revolution of 1990, Natsagdorj published the book Ruling Principles of Genghis Khan, edited by his colleague and fellow Academician Shagdaryn Bira,[3][12] which offered original arguments.