Robust control design for quantum systems has been recognized as a key task in the development of practical quantum technology. In this paper, we present a systematic numerical methodology of sampling-based learning control (SLC) for control design of quantum systems with Hamiltonian uncertainties. The SLC method includes two steps of "training" and "testing and evaluation". In the training step, an augmented system is constructed by sampling uncertainties according to possible distributions of uncertainty parameters. A gradient flow based learning and optimization algorithm is adopted to find the control for the augmented system. In the process of testing and evaluation, a number of samples obtained through sampling the uncertainties are tested to evaluate the control performance. Numerical results demonstrate the success of the SLC approach. The SLC method has potential applications for robust control design of quantum systems.