The Yangtze River Basin is among the river basins with the strongest strategic support and developmental power in China. As an invasive species, the pinewood nematode (PWN) Bursaphelenchus xylophilus has introduced a serious obstacle to the high-quality development of the economic and ecological synchronization of the Yangtze River Basin. This study analyses the occurrence and spread of pine wilt disease (PWD) with the aim of effectively managing and controlling the spread of PWD in the Yangtze River Basin. In this study, statistical data of PWD-affected areas in the Yangtze River Basin are used to analyse the occurrence and spread of PWD in the study area using spatiotemporal visualization analysis and spatiotemporal scanning statistics technology. From 2000 to 2018, PWD in the study area showed an “increasing-decreasing-increasing” trend, and PWD increased explosively in 2018. The spatial spread of PWD showed a “jumping propagation-multi-point outbreak-point to surface spread” pattern, moving west along the river. Important clusters were concentrated in the Jiangsu-Zhejiang area from 2000 to 2015, forming a cluster including Jiangsu and Zhejiang. Then, from 2015–2018, important clusters were concentrated in Chongqing. According to the spatiotemporal scanning results, PWD showed high aggregation in the four regions of Zhejiang, Chongqing, Hubei, and Jiangxi from 2000 to 2018. In the future, management systems for the prevention and treatment of PWD, including ecological restoration programs, will require more attention.