Transparent organic solar cells have recently attracted extensive interest considering their potential application for the power-generating window. By allowing the transmission of visible light while converting ultraviolet and near infrared light in the solar spectrum into electricity, transparent solar cells integrated into building facade provide a smart solution to the energy dilemma in urban area. However, current works mainly optimize the performance of solar cells for very limited incident condition, such as only considering normal incidence, which results in impractical designs for real applications. In this paper, we propose a robust design approach to achieve high-performance transparent solar cell based on a nonperiodic photonic structure considering a broad range of incident conditions representing natural sunlight illumination. Statistical performances are used in the robust design formulation and efficient sampling techniques are further employed to improve the computational efficiency. The Pareto-optimal solutions are obtained according to the multicriteria preference with respect to maximizing the expected cell transparency and the expected energy conversion efficiency, and minimizing the performance variance due to the incidence variation. As one example of the optimized design, the absorbing efficiency of the solar cell could be up to 85% that of its opaque counterpart with 32% visible light transmission and 0.13% variation coefficient of transparency under the actual solar illumination and incident angles from 9am to 3pm. By using this design methodology, practically efficient cell structure is achieved based on the location and installation orientation of the solar window.