Shaku Nihongi provides annotations to Nihon Shoki, citing many historical records including "Joguki" (Record of the Crown Prince), "Nihongi Shiki" (Private Notes on the Chronicles of Japan), "Fudoki" (description of regional climate, culture, etc.), "Kogo-shui" (History of the Inbe clan), "Tensho" (a chronological history of Japan), "Ato no Chotoko Nikki" (diary of ATO no Chitoko), "Tsukino Ohmi Nikki" (diary of TSUKI no Omi), and "Sendai Kuji Hongi" (Ancient Japanese History).
『上宮記』、『日本紀私記』、『風土記』、『古語拾遺』、『天書』、『安斗智徳日記』、『調淡海日記』、『先代旧事本紀』等、多くの史料を駆使して、注釈を付けている。