A fluidized bed membrane reactor has its great advantage in the industrial application of hydrogen production owing to good mass and heat transfer characteristics compared to a fixed bed membrane reactor. However, the concentration polarization and the densification zone formation caused by membrane permeation will restrict mass and heat transfer as well as hydrogen membrane flux. In this work, a three-dimensional simulation is carried out to investigate the hydrogen separation process in a fluidized bed membrane reactor under the Euler-Euler framework. The effects of membrane arrangements with different eccentric distances and membrane sites including internal and external membranes on concentration polarization and densification zones are discussed. The results reveal that the enhancement of eccentric distances can weaken the concentration polarization, whereas the densification zone scope is enhanced. The arrangement of internal membranes can hinder the concentration polarization and promote the hydrogen separation, while external membranes significantly influence the hydrogen removal at the bottom of the reactor.