Plant cell wall surrounding every plant cell is a highly organized polysaccharide network. Its structural complexity is dedicated to satisfy various requirements in plant growth and development. Although many genes crucial for cell wall synthesis and remodeling have been characterized, there is limited knowledge for how wall polysaccharides are organized into heterogeneous and functional structure. The vessel walls usually have spiral, reticulate, scalariform, and pitted patterns, which facilitate the physiological functions of xylem, including robust water transport and prevention of air embolism and invasion of pathogens. However, how cell wall matrix assembles to support the formation of vessel patterns is unclear. Our previous work revealed that the xylan-rich nanocompartments located at the pit boundary are indispensable for maintaining the coherence of pit patterns and vessel robustness. To identify new components that control vessel wall structure, we investigated the metaxylem vessel morphology, such as pit size and shape, in a rice variety population distributed worldwide. Genome-wide association study identified an associated interval for pit area control. Taken together with the reverse genetic studies on the developing internodes, several candidates that may be involved in the formation of vessel wall patterning have been characterized in depth. All these findings provide new insights into the assembly of vessel wall structure and offer direct targets for manipulating vessel physiology and agronomic traits.