Objective: The aim of this paper was to explore a technology which can accurately reflect the three-dimensional (3D) canopy architecture of rice plants. Method: The 3D digitizing technology was used to measure the rice plant structure in situ at the filling stage and its accuracy was evaluated. Virtual stratified-clipping method was used to analyze the rice plant architecture. Result: The 3D digitizing was an accurate method to collect the 3D coordinates of rice canopy in situ, thus quantify geometrical characteristics of rice plants. The virtual canopy, which was reconstructed according to the measured data, reflected the 3D architecture of rice in the field. The virtual stratified-clipping method could be used to accurately analyze the distribution of canopy elements in 3D space from different aspects. Appropriate virtual clipping interval should be employed in canopy architecture analysis, as too large or too small clipping interval may result in significant error or noise. Conclusion: The 3D digitizing technology and virtual stratified-clipping method are promising in quantifying the canopy architecture of rice plants.