Fluidization bed reactor is an attractive method to synthesize and process quantities of functional nanoparticles, due to the large gas–solid contact area and its potential scalability. Nanoparticles fluidize not individually but as a form of porous agglomerates with a typical porosity above 90%. The porous structure has a significant effect on the hydrodynamic behavior of a single nanoparticle agglomerate, but its influence on the flow behavior of nanoparticle agglomerates in a fluidized bed is currently unclear. In the present study, a drag model was developed to consider the porous structure effects of nanoparticle agglomerates by incorporating porous-structure-based drag laws in the Eulerian–Eulerian two-fluid model. Numerical simulations were performed from particulate to bubbling fluidization state to evaluate the applicability of porous-structure-based drag laws. Results obtained for the minimum fluidization and bubbling velocities, bed expansion ratio, and agglomerate dispersion coefficient show that, compared with the drag law of solid sphere, the porous-structure-based drag laws, especially the drag law of fractal porous spheres, provide a closer fit to the experimental data. This indicates that the pore structures have a great impact on gas–solid flow behavior of nanoparticle agglomerates, and the porous-structure-based drag laws are more suitable for describing flows in nanoparticle agglomerate fluidized beds.