The conservation of biodiversity in the Yangtze River basin is at the centre of gravity in the strategic layout of China's ecological civilisation. However, a number of factors, in particular the long-standing absence of legal protection, have caused serious damage to the biodiversity of the Yangtze River basin. The Yangtze River Protection Law, as the first special river basin law in China, provides legislative safeguards to achieve a high level of ecological protection and high-quality economic and social development in the Yangtze River basin. The Yangtze River Protection Law is goal-oriented in terms of biodiversity conservation in the river basin, and provides clear provisions and systematic arrangements for the establishment of a basin-wide coordination mechanism, the establishment of an aquatic life integrity index evaluation system, the construction of an ecological restoration and ecological protection compensation system, the conduct of biodiversity surveys and biological resources monitoring, and the in-depth promotion of fishing bans, providing a solid legal basis for biodiversity conservation in the Yangtze River basin. However, it should be noted that the construction of a biodiversity protection system in the Yangtze River basin is still in the exploratory stage, and there are practical problems in the protection of biodiversity in the basin, such as a delayed supporting system that affects the effectiveness, the lack of prominent protection functions in relocated areas, confusion in the enforcement status due to multiple enforcement bodies, and blind spots in the prevention of invasive alien species. Focusing on the above problems, this paper put forward targeted suggestions so as to speed up the reform process of the supporting system and management system, emphasise the dual role of relocation and in situ protection, improve the comprehensive law enforcement system in the Yangtze River basin, and fill the loopholes and gaps in the prevention and control of invasive alien species, with a view to providing some reference for the conservation and management of biodiversity in the Yangtze River basin.