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Shale gas reservoirs have been successfully developed due to the advancement of the horizontal well drilling and multistage hydraulic fracturing techniques. However, the optimization design of the horizontal well drilling, hydraulic fracturing, and operational schedule is a challenging problem. An ensemble-based optimization method (EnOpt) is proposed here to optimize the design of the hydraulically fractured horizontal well in the shale gas reservoir. The objective is to maximize the net present value (NPV) which requires a simulation model to predict the cumulative shale gas production. To accurately describe the geometry of the hydraulic fractures, the embedded discrete fracture modeling method (EDFM) is used to construct the shale gas simulation model. The effects of gas absorption, Knudsen diffusion, natural and hydraulic fractures, and gas–water two phase flow are considered in the shale gas production system. To improve the parameter continuity and Gaussianity required by the EnOpt method, the Hough transformation parameterization is used to characterize the horizontal well. The results show that the proposed method can effectively optimize the design parameters of the hydraulically fractured horizontal well, and the NPV can be improved greatly after optimization so that the design parameters can approach to their optimal values.