Three-dimensional (3D) multiple-input multiple-output (MIMO) system can exploit the spatial degree of freedom in vertical dimension and can significantly improve system performance compared with 2D transmission scheme. However, in the actual frequency division duplex (FDD) transmission mode, the large overhead of the reference signal and channel state information (CSI) feedback would become a barrier for performance improvement of 3D MIMO system with the significantly increased number of transmit antennas. To deal with these problems, this paper proposes a new transmission scheme of the channel state information-reference signal (CSI-RS), where the CSI-RS is precoded with 3D beamforming vectors and composed of two components: long-term CSI-RS and short-term CSI-RS. For the purpose of conducting efficient transmission in widely used FDD system, we also propose a corresponding limited channel state information feedback scheme. Moreover, multiuser pairing and scheduling criteria based on the design of the CSI-RS are proposed to realize the multiuser transmission. We have investigated multiple options for 3D MIMO codebook scheme and finally adopt the Kronecker product-based codebook (KPC) for precoding operation at the base station (BS). Simulation results demonstrate that our proposed scheme for the 3D MIMO system achieves a better tradeoff between resource overhead and throughput performance.