Rapid development of scale and functional complexity of avionics system brings higher demands on fault tolerance and reliability of Time-Triggered Ethernet (TTE). As a significant measure of fault management, reconfiguration is widely used in avionics system. Aiming at application failure because of end system module failure in TTE, a reconfiguration management strategy based on software defined networking is proposed. Then, by introducing the constraints of end system margin and resource-supply ability, a message scheduling algorithm based on Satisfiability Modulo Theory (SMT) for fault recovery is presented. The uniformity of link load and worst delay of rate-constraint messages are taken as the indexes for evaluation of the preemptive reconfiguration scheme, and an optimization algorithm is designed based on genetic theory for selection of the preemptive reconfiguration scheme. Simulation experiment verifies the validity of the message scheduling algorithm, and shows that the preemptive reconfiguration scheme after optimization has better performance.