[7] Naquin has contributed to the field of history by studying the social and cultural life of late imperial and early modern China, especially north China, including millenarian peasant uprisings, sectarian organizations, pilgrimage and temple organizations, the history of Beijing, and the material culture of the Qing dynasty.
In his review of the book for The Historian, Robert Kapp wrote, "With the aid of this extraordinary material, she has constructed an absorbing narrative not only of the founding of the rebel movement and the planning of the uprising but also of the attack on the Forbidden City...".
In a review published in the Journal of Chinese Religions, Vincent Goossaert wrote "Naquin's book, in the making for some fifteen years and long awaited by the scholarly community, is as towering, rock-solid, impressive, and memorable as its subject.
In books and articles, she discussed the emergence and endurance of the White Lotus religion, a sect that originated from Buddhist and Daoist traditions in 16th-century China, with a primary focus on its central figure, the Eternal Mother, and its growth over the subsequent four centuries.
[16] Using media from the 17th to the 20th century, she also showed how the Tanzhe Monastery and Mount Miaofeng in Beijing's suburbs, each sustained a local reputation through their history, pilgrims, and landscapes.
In an article in the Harvard Journal of Asiatic Studies, jointly written with Thomas Shiyu Li, Naquin researched the historical significance of Beijing's Baoming temple in terms of both the religion and court politics of Ming and Qing China.
She highlighted the significance of non-luxury material culture in the Ming and Qing periods, particularly that of the Greater North China Plain, and advocated for a regional perspective as a frame for lesser-known sources.