Flexible piezoelectric materials have attracted rapidly growing attention because they offer an efficient route to scavenge energies from the living environment to power personal electronics and nanosystems. Current polymer composites with low-dimensional piezoceramic fillers suffer from poor stress transfer from the polymer matrix to the active ceramic fillers, thus significantly limiting the energy harvesting performance. Herein, an interconnected 3D piezoceramic skeleton has been developed by a biofibril template method using the newly developed rare-earth Samarium-doped Pb(Mg 1/3 Nb 2/3 )O 3 -PbTiO 3 (Sm-PMN–PT) for flexible piezoelectric polymer composites. When subjected to external mechanical stimulation, the 3D interconnected structure results in effective stress transfer, and consequently, greatly enhanced energy harvesting output. The 3D piezocomposite shows the open-circuit output voltage and short-circuit current density up to ~ 60 V and ~ 850 nA cm −2 , respectively, with the maximum instantaneous power density of ~ 11.5 µW cm −2 which is ~ 16 times higher than that of the conventional nanoparticle-based composite. The remarkable enhancement in the tress transfer ability and piezoelectric response of the biofibril-templated 3D structure have also been verified by phase-field simulations. This work provides a promising paradigm for the development of high-performance flexible energy harvesting materials.