Highly anisotropic thermal conductivity, i.e., a limited through-plane thermal conductivity (λ⊥), is normally observed in polymer composites with asymmetric fillers that are vulnerable to orientate along the flow field during melt-processing. We herein explored the possibility to tailor the filler arrangement and λ⊥ of polymer composites with asymmetric fillers using nonconductive hollow glass microspheres (HGμS). The results showed that λ⊥ of ultrahigh-filled polyamide 6/flake graphite (PA6/FG) composites with 70 wt% (54.7 vol%) FG increased by 27% instead of decreasing when replacing 3 wt% FG platelets with HGμS (i.e., 8.1 vol%, and 12.2 vol% HGμS with a diameter of 18 μm and 38 μm, respectively). The increase of λ⊥ from diluting FG with HGμS was attributed to the reduced structural anisotropy of the FG network, i.e., the in-plane orientation of FG platelets within the polymer matrix was inhibited. A synergistic effect on the improvement of λ⊥ was achieved by replacing FG platelets with combination of HGμS and alumina (Al2O3) microspheres. This synergy takes the effects from the “bridging” of FG platelets by Al2O3 and the inhibiting of in-plane FG orientation by HGμS.