Seed shattering in naked oat (Avena nuda) is a severe problem, resulting in significant yield losses. In the present study, the seed-shattering rates were characterized in a set of 177 naked oat cultivars and lines. Eight cultivars with different seed-shattering rates were studied in several morphological and physiological traits that may be related to seed shattering at different developmental stages. Three types of paleas, viz. boat type, defect type and flaky type, were identified at the dough stage, and the proportion of the boat-type paleas were found to positively correlate with seed shattering. In a following scaling-up morphological study on paleas and lemmas in 32 cultivars with different seed-shattering rates, the length, width and the thickness of paleas and lemmas were investigated, and the ratio of the bottom/medium thickness of both paleas and lemmas showed high association with seed shattering tolerance in naked oat. These indicate that the architecture of paleas and lemmas has a particularly obvious correlation with seed shattering in naked oat. More intriguingly, a unique zigzag pattern of the cell wall was found in lemma tissues of naked oat, which may increase the toughness and strength of lemmas and help with seed retention.