Five rice cultivars were applied for investigating effect of milling degree on rice physicochemical properties. The first layer had the lowest peak viscosity, followed by the second and third layers, indicating the effect of non-starchy components on starch gelatinization behaviors. Consistently, more content of non-starch components in the first layer led to an enhanced gelatinization temperature. Rheological study demonstrated the G’ and G” were successively increased as the layer moved inward, indicating a stronger gel network due to the increased amylose content and crystallinity in the corresponding layer. This is the first study to reveal the second layer has the highest digestibility, suggesting both non-starch components and starch structure control starch digestion. Furthermore, analysis of volatile compounds found alcohols and ketones concentrated in the first layer, whilst compounds including (E,E)-2,4-decadienal, 3-octanone and 3-nonen-2-one only existed in the second layer, serving as an indicator for managing the rice quality during milling.