The method of root box was adopted to cultivate flue-cured tobacco. Two fertilizer treatments of high phosphorus and low phosphorus were designed to investigate the effects of high phosphorus and low phosphorus on physiological characteristics, rhizosphere microbe quantity and root configuration of flue-cured tobacco. The results showed that tobacco growth index (plant height, stem width, leaf weight, root weight), physiological index (Pn, NAR, root activity), rhizosphere microbe quantity (bacteria, fungi, actinomyces) under high phosphorus treatment were all higher than low phosphorus treatment. Root configuration under high phosphorus treatment and low phosphorus treatment had their own distinct rooting traits and emphasis respectively, the superiority of root configuration under high phosphorus treatment occurred at the third round root and surface lateral root in late tobacco growth stage, but low phosphorus treatment occurred at the first round, the second round and total adventitious root. The amount of adventitious root under low phosphorus treatment was higher than high phosphorus treatment.