Optimal partitioning theory suggests that plants would allocate biomass to the organ that acquires the most limiting resources, while root system architecture varies with ontogeny and environmental conditions. Detailed analysis of biomass allocation, organ morphology and root system architecture in hydroponically grown rice plants were performed to investigate the impact of phosphorus deficiency on coordination and allometric relationship between shoots and root system and root system architecture. The result indicated that P deficiency resulted in preferential biomass allocation to roots, and the shift in allocation was due to the true phenotypic plasticity, rather than ontogenetic drift. The root system showed a greater phenotypic plasticity than shoot system in response to P deficiency. The changes in root architecture improve the capabilities for both exploration and absorption. In terms of development, there was a synchronization between root and shoot growth even in the case of P deficiency.