Two rice cultivars Wuyunjing 7 (Al-tolerant) and Yangdao 6 (Al-sensitive), differing sharply in aluminum tolerance, were selected as subjects in a hydroponic experiment to investigate effects of P on growth of the rice seedling under Al stress and relationship between Al tolerance and P efficiency of the rice through alternation of Al and P treatments for two weeks. Results show that in the aspect of biomass and root parameters, P application alleviated toxic effects of Al on both cultivars. The concentration of P was obviously higher in Cultivar Wuyunjing 7 than in Cultivar Yangdao 6, while the concentration of Al in root was lower in the former than in the latter, and as a result, the P/Al ratio was significantly higher in the former than in the latter. However, though the two cultivars did not differ in Al concentration in the root surface and inter-root free space, Cultivar Wuyunjing 7 was significantly higher than Cultivar Yangdao 6 in P concentration therein, demonstrating that the rice cultivar, high in Al tolerance, is higher in capability of its apoplast of detoxifying Al, which may be related to the higher P uptake efficiency of Wuyunjing 7. In addition, compared with Wuyunjing 7, Yangdao 6 was though lower in P uptake efficiency, it was higher in P utilization efficiency, which suggests that the Al tolerances of the two cultivars do not consist with their P uptake efficiencies and P utilization efficiencies, which may serve as a theoretical basis for selecting and breeding rice seeds for paddy fields of acid soil, that is to say, to select and breed rice of genotypes suitable to acid paddy soils, it is essential to focus on Al tolerance and P utilization efficiency as well.