The discovery and separation of the PROSTRATE GROWTH 1 gene has significantly contributed to reveal the molecular mechanism of rice evolution and has aided the study of the molecular basis of rice plant architecture. However, the influence of the PROSTRATE GROWTH 1 gene on canopy structure characteristics has not been quantitatively evaluated, especially when the canopy was fully covered. Three-dimensional digital technology was used to reconstruct the three-dimensional canopies of two rice varieties with PROSTRATE GROWTH 1 contrasting gene (Teqing with erect growth habit and YIL18 with prostrate growth habit) in three main growth stages (booting stage, heading stage and grain filling stage). The effects of the PROSTRATE GROWTH 1 gene on the canopy structure characteristics were quantitatively evaluated using the virtual layer cutting method. The results showed that YIL18 had the prostrate growth tendency with lower height of canopy, more tillers, narrower leaves and smaller leaf area index, when compared with those of Teqing. The tiller angle (the angle between the tiller and the horizontal plane) was reduced from 77.5° to 62.8°, 83.8° to 75.0° and 83.4° to 77.2° at the three growth stages, respectively, and the mean leaf inclination angle decreased from 66.2° to 44.3°, 74.9° to 64.2° and 76.0° to 68.3° contrasting Teqing with YIL18. Meanwhile, the leaf inclination angle for YIL18, which accounted for the maximum proportion at the upper parts of the canopy, was one grade (10°) lower than that of Teqing. Furthermore, the spike grain number and thousand seed weight of YIL18 were significantly less than those of Teqing but the spike number was more than that of Teqing (P < 0.05). Overall, the PROSTRATE GROWTH 1 gene had a significant impact on the canopy structure of rice. Our study assessed the influence of the PROSTRATE GROWTH 1 gene on the canopy structure of rice quantitatively and has provided a reliable scientific basis for future breeding programs.