MC1R gene is the key gene that determines the color of animal hair. The melanocortin receptor gene of Nubian goat (white, pure black and brown flower) was cloned and analyzed by systematic bioinformatics. The result showed that the coding region of the MC1R gene of Nubian goat was 954 bp in length and encoded 317 amino acids. The results of multiple sequence comparison showed that the clones were 99%, 87%, 86%, 85%, 84%, 81%, and 77% similar to the published pig, cow, human, dog, sheep, mouse, and chicken, respectively. It showed that MC1R gene had a high conserved type among different species. The goat MC1R protein has a molecular mass of 34.65 ku, an isoelectric point of 8.70, which is weakly alkaline, and contains seven transmembrane domains typical of cell membrane receptor proteins. Sequencing analysis of the black, brown and white different color MC1R genes of Nubian goats revealed that there are three SNPs in the gene sequence, which are 219, 712 and 1160, respectively. The C/T mutation did not cause amino acid mutations; base A/G mutations occurred at position 712 and caused amino acid mutations in pure black and brown goat samples, which were mutated from tryptophan to cysteine. The results of this study have important reference significance for the future correlation analysis between MC1R gene and Nubian goat wool color traits and the color genetic mechanism of Nubian goats.