The yield potential of japonica/indica hybrids (JIH) has been achieved over 13.5 t ha–1 in large-scale rice fields, and some physiological traits for yield advantage of JIH over japonica inbred rice (JI) and indica hybrid rice (IH) were also identified. To date, little attention has been paid to morphological traits for yield advantage of JIH over JI and IH. For this reason, three JIH, three JI, and three IH were field-grown at East China (Ningbo, Zhejiang Province) in 2015 and 2016. Compared with JI and IH, JIH had 14.3 and 20.8％ higher grain yield, respectively, attributed to its more spikelets per panicle and relatively high percentage of filled grains. The advantage in spikelets per panicle of JIH over JI and IH was shown in number of grains on the upper, middle, and lower branches. Compared with JI and IH, JIH had higher leaf area through leaf width and lower leaf angle of upper three leaves, higher leaf area index and leaf area per tiller at heading and maturity stages, higher stem weight per tiller and K and Si concentrations of stem at maturity, higher dry matter weight in leaf, stem, and panicle at heading and maturity stages, and higher biomass accumulation after heading and lower biomass translocation from stem during ripening. Leaf width of upper three leaves were correlated positively, while leaf angle of upper three leaves were correlated negatively with biomass accumulation after heading, stem weight per tiller, and per unit length. Our results indicated that the grain yield advantage of JIH was ascribed mainly to the more spikelets per panicle and relatively high percentage of filled grains. Higher leaf area through leaf width and more erect leaves were associated with improved biomass accumulation and stem weighing during ripening, and were the primary morphological traits underlying higher grain yield of JIH.