Fusarium crown rot (FCR), mainly caused by Fusarium pseudograminearum, is a serious soil-borne disease resulting in large yield loss in many arid and semi-arid areas in the world. Under drought conditions, it is very important for plants to have a healthy and strong root system to obtain enough water and nutrition to maintain yield. It was previously reported that root architecture traits may be significantly affected by FCR infection. The defense mechanisms of wheat root to FCR is poorly understood. In the study, we carried out a comparative transcriptomic analysis at multiple time points on the FCR resistant and susceptible varieties inoculated with F. pseudograminearum. A rapid and high amplitude transcriptome reprogramming was detected during FCR infection. Genes responsive to FCR infection in the roots are mainly involved in the regulation of phenylpropanoid biosynthesis, plant hormone signal transduction and root development etc. The hormone quantification in root during FCR infection showed that plant hormones have important roles on FCR resistance. The exogenous hormones treatments confirmed the results from these studies. Our results revealed the differential roles of plant hormones on root growth under FCR infection.