Phosphorus is the second most important macronutrient after nitrogen and it has many vital functions in the life of plants. Most soils have a low available P content, which has become a key limiting factor for increasing crop production. Also, low P use efficiency (PUE) of crops in conjunction with excessive application of P fertilizers has resulted in serious environmental problems. Thus, dissecting the genetic architecture of crop PUE, mining related quantitative trait loci (QTL) and using molecular breeding methods to improve high PUE germplasm are of great significance and serve as an efficient approach for the development of sustainable agriculture. In this review, molecular and phenotypic characteristics of maize inbred lines with high PUE, related QTL and genes as well as low-P responses are summarized. Based on this, a breeding strategy applying genomic selection as the core, and integrating the existing genetic information and molecular breeding techniques is proposed for breeding high PUE maize inbred lines and hybrids.