Hypoxia tolerance, one of the important goals of fish breeding, is beneficial for aquaculture and the transporting of fish. Based on the bisexual fertile allotetraploid crucian carp hybrid lineage obtained by distant hybridization, we successfully developed the allotriploid crucian carp via interploidy crossing with diploid red crucian carp. This allotriploid fish exhibited obvious hypoxia tolerance with lower values of dissolved oxygen at Pcrit (critical oxygen press) and 50 % ASR (aquatic surface respiration) than its original parents. Hemoglobin is the main vector of oxygen in vivo. This study examined the changes in amino acid sequences and natural protein conformation of hemoglobin, and found that the Hbα sequences of allotriploid crucian carp displayed obvious hybridity, including recombination and variation, when compared with its original parents. Moreover, the expression of hbα gene is higher in the liver and blood of allotriploid crucian carp than in its original parents. After acute anoxia treatment, the expression of gata1 gene, which served as the general switch for erythroid development, decreased in the blood of all the three kinds of fish. However, only in the allotriploid crucian carp hbα gene expression significantly decreased, coupled with the erythrocytes displaying an increased ratio of nuclei/cytoplasm. Taken together, this study suggested that changes in hemoglobin coupled with the erythrocyte morphological alterations under hypoxia increased the hypoxia tolerance ability of allotriploid crucian carp, which would provide a new perspective to guide fish breeding to obtain high-quality fish species with increased hypoxia tolerance.