The treatment effects of the blue algae outbreak in Taihu Lake and the existing problems and its reasons were analyzed. The objective of eliminating eutrophication and eliminating blue algae outbreaks in sub-waters before 2049 and the integrated technical countermeasures to achieve the objective were proposed, including three major measures of eliminating eutrophication, eliminating blue algae outbreaks and restoring wetlands. It is suggested that the plan for comprehensive water environment management in the Taihu Lake River Basin should be revised once more so that the current eutrophication control in the Taihu Lake can be transferred to a stage where the treatment of eutrophication and the elimination of blue algae outbreaks are both important.