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The architecture of rice roots is the spatial configuration of its roots, which shows a high diversity. To explore the architecture and distribution characteristics of rice roots，hydroponics method experiments were conducted to measure three dimensional spatial coordinates and morphological parameters of rice roots at different growth stages, which quantified the structure of rice roots with high accuracy. After analyzing the experimental data， the initial position of the root node, growth direction of branches and the root growth function were determined. Three dimensional growth modeling of rice roots based on differential L-system was proposed to describe its growth rule by analyzing the topological structure and quantifying their biological characteristics, and the output accuracy of the model was tested. Visual C++ and OpenGL standard graphics library were used to implement the threedimensional visualization simulation system for rice root growth，and the dynamic growth process of rice roots was visually reproduced. Analysis results indicated that the average simulated fitness of the total root length, surface area and volume were about 96.82%, 95.86% and 93.96%, respectively. Therefore, the model can express the morphological characteristics and growth rules of rice roots at different growth stages, and the results may form a base for forthcoming study on the relationship between morphological structure changes of rice roots at different growth stages and their physiological and ecological factors.