Lake Taihu and Taihu Basin play an increasingly important role in the implementation of the national strategy of the integrated development of the Yangtze River Delta(YRD) region. In the context of the high-quality development of regional integration, the management of Lake Taihu is facing more new, complex and difficult challenges. It highlights two aspects of the water environmental improvement and water resource supply. In detail, the separate management measures on lake and land cannot effectively solve the water problems, the management responsibility divided by administrative areas fails to meet the new requirements of regional integration, and the lack of mechanism of environmental integrated protection/harness and water resources protection/sharing, all of which actually become obstacles to the integrated development of the YRD region. This paper believes that the water deterioration of Lake Taihu is not limited to Lake Taihu itself but closely related to the Taihu Basin and the intensive human activities around. To promote the high-quality integrated development of the YRD region, the systematically management and governance of Lake Taihu should be improved out linking with the perspective of lake-basin system. It means to form a multi-factor coordination of resources, environment, ecology, society, and economy etc, and to achieve a coordinated management of land exploitation and water protection and a trade-off among economic, social and natural benefits in different sub-regions. Therefore the paper suggests several practical ways:First, the government concerned should explore the way to manage the complex lake-basin system with multiple factors, so as to promote the innovative thinking on the regional ecological and environmental integration; Second, put more effort on the research, development and application of key technology of lake-basin harness, and on the formation of comprehensive scientific system of lake-basin process simulation, evaluation and management, so as to promote the technological and scientific innovation in the field of ecological environment; And third, explore the mechanisms of resource and environmental protection/harness/sharing cooperation, and green development modes as well, so as to promote the institutional innovation of the integrated development.