It is well known that there is inherent radiation pattern distortion for the commercial base station antenna array, which usually needs three antenna sectors to cover the whole space. To eliminate pattern distortion and further enhance beamforming performance, we propose an electromagnetic hybrid beamforming (EHB) scheme based on a three-dimensional (3D) superdirective holographic antenna array. Specifically, EHB consists of antenna excitation current vectors (analog beamforming) and digital precoding matrices, where the implementation of analog beamforming involves the real-time adjustment of the radiation pattern to adapt it to the dynamic wireless environment. Meanwhile, the digital beamforming is optimized based on the channel characteristics of analog beamforming to further improve the achievable rate of communication systems. An electromagnetic channel model incorporating array radiation patterns and the mutual coupling effect is also developed to evaluate the benefits of our proposed scheme. Simulation results demonstrate that our proposed EHB scheme with a 3D holographic array achieves a relatively flat superdirective beamforming gain and allows for programmable focusing directions throughout the entire spatial domain. Furthermore, they also verify that the proposed scheme achieves a sum rate gain of over 150% compared to traditional beamforming algorithms.