Three-dimensional structures of RNA-protein complexes are crucial for understanding their diverse functions. However, the number of the RNA-protein complex structures solved by experiments is still limited at present. To solve this problem, some computational protocols have been proposed to predict three-dimensional RNA-protein complex structures. But the prediction accuracies of these protocols are lower. The reason may be that these protocols don't fully incorporate the features of RNA-protein interfaces. Here we propose a novel computational protocol for three-dimensional RNA-protein complex structure prediction, 3dRPC, which applies new schemes to the discreteness of molecule and charge in docking algorithm and the construction of the reference state in scoring function in order to take account of the features of RNA-protein interfaces. This protocol achieves a high accuracy comparable to the well-developed algorithms for three-dimensional structure prediction of protein-protein complexes when tested on a RNA-protein docking benchmark.