We present a novel approach to harness the oscillation energy from cilia in chaotic flow to enhance scalar transport, addressing limitations of the laminar boundary layer. In contrast to the scallop theorem, where reciprocal motion yields negligible transport, coordinated rigid cilium oscillations in chaotic flow trigger boundary-layer resonance, significantly boosting scalar transport at specific frequencies. Under relatively high rigidity, the cilia undergo only small elastic deformations at the driving frequency, and their strokes remain nearly time symmetric. Nevertheless, unlike the classical expectation that reciprocal motion yields negligible transport, coordinated rigid cilium oscillations in chaotic flow trigger boundary-layer resonance, producing a sharp, frequency-selective boost in transport. At low to medium frequencies, cilium-driven fluid displacement enhances transport via vertical mixing. Above a critical frequency, rapid cilium motion induces unstable shear flow, generating coherent vortical structures that amplify mixing in chaotic flow regimes. These vortices, which interact with the inherent coherent structures of the chaotic flow, dramatically improve the efficiency of transport. Our findings reveal a dynamic coupling between cilium-driven resonance and chaotic flow coherent structures, providing a paradigm for optimising transport in thermal systems through active flow control.