Branched spike wheat is a hexaploid wheat with branched rachis on its main rachis, and branched rachises in the shoot apex occur and develop just after the two ridges stage. In this study, dynamic changes of four endogenous plant hormones [indole-3-acetic acid (IAA), gibberellic acid (GA), abscisic acid (ABA) and zeatin riboside (ZR)] and the expression of a hormone-related gene were measured among wheat lines with different genotypes and spike morphologies. It is a basis for further exploring the developmental mechanisms of branched spike and for breeding new wheat lines with more spikelets and grains. A group of near isogenic lines (NILs), including one branched spike line, and three normal spike type lines was sampled at four time points from the end of two ridges stage to the floret differentiation stage. The endogenous hormones in young shoots, young leaves and tillering nodes in these lines were measured and the expressions of TaIAR3, encoding IAA amide hydrolase which involvs in the IAA synthesis was detected. The results showed that the contents of IAA exhibited a significant different pattern in branched spike line from those in normal spike lines, while the contents of GA, ABA and ZR showed similar change patterns. The expressions of TaIAR3 were also significantly different between branched spike line and normal spike lines. Both the IAA content and TaIAR3 expression in branched spike wheat were much higher than those in the normal spike lines. These results suggest that quantitative changes in auxin may correspond to different spike morphology. Higher IAA content and TaIAR3 expression might be benefical for promoting the formation and elongation of branched rachis in branched spike wheat line.