Abstract The guerrilla warfare behind enemy lines of the national government is still a weak link in the study of the history of the war of resistance, and the naval guerrilla warfare on the Yangtze River is even less specifically discussed. This paper first analyzes the change in the national government’s naval operational thinking after the July 7 Incident and up to the Battle of Wuhan and divides the naval operations in the Yangtze River Basin during the period of total war of resistance into four stages. Then, combined with the ontology theory and taking various archives, museums, libraries, and memorial halls as sources, after fusing heterogeneous data, it adopts the relevant writings, notes, diaries, speeches, photographs, objects of the Navy’s Yangtze River Resistance as well as the results of the archive compilation formed later to construct the Navy’s Yangtze River Resistance Archives Knowledge Graph Model. After the reasoning and searching of the knowledge map, it is concluded that in 1938 and 1940, the Yangtze River Bray Guerrilla Group killed 950 and 3020 enemies, respectively, destroyed 20,400 tons and 118,400 tons of warships, strongly supported the Battle of Wuhan and two Battles of Xiangbei, and prevented the Japanese army from invading to the west along the river, and in 1940, it destroyed the Japanese large-scale transports and merchant ships of a total of 58,700 tons, which dealt a heavy blow to the Japanese army on the Yangtze River and the Yangtze River. Heavy blows to the Japanese water transport capacity of the Yangtze River delayed its front and rear troops, weapons, supplies, and transportation plans so that its ability to expand received a major limitation, unable to continue the attack on the Yangtze River west of Wuhan, to defend the safety of Chongqing and Sichuan. This paper makes up for the research gaps in the history of the National Government’s naval resistance and the history of guerrilla battles in the Bray of the Yangtze River Basin and provides a useful exploration of the combination of resistance history research and information technology.