Rhizosphere is not only the gateway for soil nutrients entering plants, but also the microzone for the interaction among plant, soil and microorganisms. Rhizosphere determines the supply strength and effectiveness of nitrogen and phosphorus, which in turn affects the nutrient use efficiency and crop productivity. The recent progress of research on the synergy transformation and transportation of nutrients in soil-root-microbe systems was reviewed. The factors driving the change of microbial community composition relative to the turnover of nitrogen and phosphorus were investigated at different spatial-temporal scales. The signal network regulating the formation of arbuscular mycorrhizal systems and the genetic control mechanisms to affect the translocation of nitrogen and phosphorus were studied. The ecophysiological response mechanisms of the roots adapting soil nutrient conditions were revealed by signal networks, root exudates regulating root growth, and the relationship between crop root architecture and nitrogen and phosphorus use efficiency. In the future, we need to deepen our knowledge of soil-root-microbial synergy mechanisms at the differently interfaces by studying: 1) the distribution pattern and succession law for microbial food web and its key function groups in rhizospheres and soil aggregates; 2) the impacts of root architecture on the functions of root-microbe coordination system, and the regulatory mechanisms for root proton secretion and nutrient transport proteins on root growth and nutrient uptake under the nutrient deficient conditions; and 3) the signaling networks and their impacts on nutrient use for known signals (such as strigalactone and N-acyl-homoserine lactones (AHLs) and new signal substances (such as microRNA). Finally, the biological regulatory pathways and countermeasures should be proposed to increase the utilization efficiency of nitrogen and phosphorus under different climate, soil and crop regimes.