Based on pot experiment, the rice grown under dryland cultivation is selected to study the effects of phosphorus on seedling growth, root morphology, phosphorus uptake and physiological phosphorus use efficiency. Results showed that the application of phosphorus fertilizer promoted the growth of shoot and root of rice, the stress of phosphorus deficiency significantly increased the ratio of root to shoot, and there was significant genotypic variation in this ratio, the ratio of root/shoot under low phosphorus level and high phosphorus level was 1.982 for Cong-ai 2 cultivar and 1.096 for Huang-hua-zhan cultivar, respectively. With the increase of phosphorus concentration, phosphorus content in rice increased, whereas physiological phosphorus use efficiency decreased in the five rice cultivars. Under three phosphorus levels, phosphorus content of 3345 cultivar was higher but physiological phosphorus use efficiency was lower than other four cultivars. Further correlation analysis between root growth, phosphorus uptake and physiological phosphorus use efficiency showed that root length was significantly correlated to phosphorus content of rice. The application of phosphorus fertilizer can coordinate the relationship between root and shoot, and can promote the growth of root system and phosphorus content in plant.