The traditional design method of the geomembrane seepage-proofing canal with soil protective layer only considers the reliability on single hydraulics conditions, and neglects the practicability on economy. Based on the multi-objective fuzzy optimization theory, the section of the geomembrane seepage-proofing canal with soil protective layer was optimized. A multi-objective fuzzy optimal mathematics model whose goals consist of economical efficiency and transportation ability and which satisfies the given conditions was established. The fuzzy optimal results of canal design parameters in different submergence-degree conditions were given by optimizing the section structure of seepage-proofing canal with soil protective layer geomembrane. Effects of design parameters, such as canal slope angle, width of canal bottom, height of canal, thickness of soil layer, on the whole goal level were analyzed by simulation analysis. The research results supply the reference to raise the whole design level of the geomembrane seepage-proofing canal with soil protective layer.