To screen the single nucleotide polymorphism (SNP) loci and candidate genes associated with low-phosphorus stress in wheat, genome-wide association study (GWAS) of low-phosphorus related traits in common wheat was performed for understanding the genetic mechanism of low-phosphorus tolerance. In the study, 198 wheat varieties (lines) originated from the Huang-Huai area were used as test materials to evaluate the related traits in low phosphorus and normal phosphorus solution cultures. The wheat 35K Chip with 11896 SNP markers which were distributed in the whole genome of wheat were used to analyze the related traits of low-phosphorus tolerance. The mixed model of Q+K was chosen to determine the statistical associations between phenotypes and genotypes to evaluate the effects of population structure and related traits. The result showed that the low-phosphorus tolerance character of wheat had a wide range of phenotypic variation with the coefficient variation between 15.65% and 26.59%. The polymorphism information content (PIC) was between 0.095 and 0.500. Population structure analysis showed that the natural population in the experiment could be divided into two subgroups. GWAS analysis indicated that 67 SNP loci were significantly associated with low-phosphorus tolerance (p ≤ 0.001), which were located in 18 chromosomes except 3A, 3B and 3D chromosomes. Each SNP could explain 5.826% - 9.552% of phenotypic variation. Four SNP sites were simultaneously associated with 2 different low-phosphorus tolerance traits in these significant sites. Seven candidate genes may be related to the low-phosphorus tolerance of wheat through analysis of the 67 SNP sites. TraesCS6A02G001000 and TraesCS6A02G001100 play important roles in the synthesis of zinc finger. TraesCS6A02G118100 may be induced by low-phosphorus stress. TraesCS5D02G536400, TraesCS1B02G154200 and TraesCS5D02G536500 are related to the family of low-phosphorus stress-related enzymes. TraesCS1D02G231200 is related to DUF538 and its product can be a putative candidate for common stress-related protein in plant.