Plants have evolved a conduit system with reinforced wall and innovative wall structures that ensure efficient transport of water and nutrients. Vessel pits, fine three-dimensional (3D) cavities in conduit walls, are key determinants of plant hydraulics and growth plasticity. However, their ultrastructure and formation mechanisms are unknown. Here, we reveal the nanoscale 3D structure of pits and the molecular pathway that mediates pit shaping and sustains xylem robustness and grain yield. A quantitative trait locus for pit size (PS1), identified by a genome-wide association study in rice, is a xylan deacetylase that controls pit geometry. An elite PS1 allele modifies xylans to a hypoacetylated state, facilitating their binding to cellulose and maintaining wall coherence around pit boundaries. The elite haplotypes confer rice varieties with promoted nitrogen transport and grain yield. We thus discover a molecular pathway that boosts xylem hydraulics and crop yield, offering a promising strategy for sustainable agriculture.