Nitrate transport protein, ZmNRT1.1B, plays an important role in nitrate absorption and transport in maize root. The sequence polymorphism of ZmNRT1.1B is a key for understanding the biological function of ZmNRT1.1B and developing molecular markers for efficient utilization of nitrogen fertilizer. In this study, database mining and coding regions sequencing were used to analyze the polymorphisms of ZmNRT1.1B coding regions in 507 inbred lines from an association analysis genetic population and 60 maize inbred lines. The results showed that most of the mutant sites were identified in the 5’-UTR regions and intron regions of ZmNRT1.1B. The coding region of ZmNRT1.1B was highly conserved. Only 29 SNP sites and 1 InDel site were found in the coding sequence of 1,788bp, of which 23 synonymous mutations and 6 non-synonymous mutations were found. According to the sequence variation of the coding regions or the amino acid sequences translated from the coding regions with non-synonymous mutations and the InDel site, 60 maize inbred lines were divided into 20 haplotypes or 8 haplotypes, respectively.The homologous modeling results showed that the mutation of Asp286Ala in amino acid sequence and the insertion of Ala at 292 could lead to the change of protein folding and change the structure of the protein.