Despite decades of intense research efforts on the self-assembly of nanoparticles in mesophase-forming copolymers, the progress in practical applications is impeded by the lack of knowledge about the dynamic transition of such hierarchical nanostructures in an environment bearing an external load. Here, we show that the hierarchical self-assembly of nanoparticles in block copolymer scaffolds can be made to significantly alternate by external compression, characterized by a continuous and reverse transition among various distribution states of nanoparticles in their preferential domains. Theoretical analysis reveals that compression-induced transition of the nanoparticle distribution can be fundamentally attributed to unique entropic effects originating from the compacted block chains. Further, we demonstrate that the hierarchical nanostructures with different distribution states of nanoparticles can lead to mechanomutable phonon transport properties. The findings reveal the mechanoresponsive behaviors of the hierarchical nanostructures of block copolymer-based nanocomposites and their potential applications as thermal interface materials with tailored thermal conductivity.