Composite films composed of μm-sized hexagonal boron nitride (hBN) flakes and polyimides (PIs) having (a) rigid (sBPDA-PPD, sBPPD) and (b) flexible (sBPDA-ODA, sBPOD) molecular structures were fabricated to investigate the effects of PI chain structure on the morphological structures as well as in-plane and out-of-plane thermal diffusivity (TD// and TD⊥). SEM and WAXD measurements revealed that the two types of composites differ significantly in the void concentration (ϕv) and the hBN/PI interfacial affinity. The sBPPD composites exhibited smaller ϕv than sBPOD. However, delamination, which was rarely observed at the hBN/sBPOD interface, was found at the hBN/sBPPD interface. These differences are attributed to the structure of PI chains: rigid chains of sBPPD generate dense interchain and polymer-filler packing owning to their small free volume, but relatively high shrinkage rate during curing results in delamination. The sBPPD composites exhibited large anisotropy in TD// and TD⊥, reflecting the in-plane orientation of sBPPD chains. At higher hBN content, the sBPOD composites exhibited a smaller TD⊥ increase due to an increase in ϕv. In addition, it was demonstrated that the TD⊥ is effectively increased by enhancing the relaxation of PI chains by removing the constraint from the substrate during thermal curing.