The search for new thermoelectric materials has gained rapid progress in recent years as thermoelectric technology offers the potential for environmentally friendly and sustainable energy conversion methods from waste heat to electricity. Using first-principles calculations based on density functional theory we show that bonding hierarchy gives rise to high thermoelectric performance in BaAu₂P₄, a layered Zintl compound with a small band gap. BaAu₂P₄ exhibits crystallographic heterogeneity in which rigid [Au₂P₄]²⁻ units are separated by layers of Ba²⁺ cations, which are bonded relatively weakly to the lattice through electrostatic interactions. While the covalently bonded chains of phosphorus atoms facilitate large electrical conductivity, the presence of multiple bands near the Fermi level gives rise to an enhanced Seebeck coefficient. On the other hand, the loosely bound Ba along with the heavy Au atoms strongly scatter the heat carrying acoustic phonons, inducing a very low lattice thermal conductivity along the stacking direction. As a consequence of this coexisting rigid and fluctuating sublattices, BaAu₂P₄ exhibits a large power factor and low lattice thermal conductivity, which results in a high thermoelectric figure of merit (zT).