Heterogeneity among grape berries directly affects wine quality and restricts the wine grape industry’s development. To study the heterogeneous development of Vitis amurensis berries, the morphology and physiology of three different types—large berry, medium berry, and live green ovary (LGO)—in the same clusters of wine-making cultivar ‘Shuangfeng’ were monitored at different growth stages from June to September. External differences in berry development were distinguishable at 12 days after full bloom (DAF). The pedicel, berry size, fresh weight, and seed length of the medium berries were intermediate between those of large berries and LGOs. Seeds are crucial for fruit set and normal berry development. The activity levels of soluble acid invertase and cell-wall-bound acid invertase in large berries increased earlier, at 18 DAF, than the accumulation of sugar. Abscisic acid concentrations in medium berries and LGOs were greater than that in large berries at 18 DAF. The greater endogenous indole-3-acetic acid concentration in the medium berries compared with LGOs might protect the former from abscission.