Fractal nanoparticle agglomerates (FNPAs) have radially inhomogeneous permeability distribution, and their shielding effects are different from those on solid particles and homogeneous permeable particles. This paper presents the first numerical simulation with radially varying permeability model to investigate the effects of average dimensionless permeability (Da), Reynolds number (Re), and dimensionless separation distance (L*) on the shielding effect of FNPAs. Three typical shielded arrangement cases for identical FNPAs aligned streamwise in a uniform free stream with Re = 30−250 are considered. The results reveal that shielding effects are significantly affected by the arrangements, and strong swallowing phenomena, rarely reported in homogeneous permeable models, are observed at higher Re and smaller L*. The shielding effect of FNPAs with radially varying permeability is ∼70% lower than that with the homogeneous permeable model at Da = 10 −4 −10 −2 , and the maximum deviation from the solid sphere model is up to ∼73%. Radially varying permeability of FNPAs should not be ignored. Further inference is given that FNPAs are easier to form mesoscale clusters than solid particles in gas−solid heterogeneous flows. This work employs a more realistic model and provides a theoretical basis for a comprehensive study of the interaction mechanisms between FNPAs in dense gas-nanoparticle flows.