Influenced by the international standard contract conditions such as the FIDIC, the engineering and theoretical circles in China often connect the engineering general contract with the fixed price contract and its simple governance structure, which restricts its application and popularization in construction of water conservancy projects with uncertain site data invested by the government. The content of the engineering general contract is analyzed. It is pointed out that the largest advantage of engineering general contract is its integration of design and construction for a contractor so as to provide power, platform and space for the contractor to optimize the project and further to obtain added value of the project. For implementing the engineering general contract of water conservancy projects, the corresponding transaction mode should be innovated to adapt to their particularity and to give full play of their value-added advantage. The status of worldwide engineering general contract is analyzed, and some key scientific issues for the mode innovation of engineering general contract of water conservancy projects in China are put forward, mainly including project identification, mode design, distribution of added value and optimization of governance system at levels of owner and contract.