Enhancing nutrient efficiency in crops is a critical goal for sustainable and environmentally friendly agriculture. Among the 17 essential elements required for plant growth, nitrogen (N) and phosphorus (P) are particularly significant. Limited availability of these nutrients in soils poses a major challenge to crop growth and productivity, making the improvement of nutrient efficiency a top priority. Root system architecture, which refers to the three-dimensional configuration of roots in the soil, plays a pivotal role in a plant's ability to access soil nutrients. Additionally, symbiotic relationships between plants and microorganisms such as arbuscular mycorrhizal fungi or rhizobial bacteria further enhance nutrient acquisition. This review highlights recent progress in understanding how crop species regulate root architecture in response to nutrient levels and microbial symbioses through genetic or QTL (quantitative trait loci) mechanisms, ultimately improving nutrient uptake efficiency.