In this paper, the Graphics Processing Unit(GPU) computing together with Cluster of Workstations(COW) techniques are discussed. Based on which a high efficiency hardware accelerated Finite-Difference Time-Domain (FDTD) algorithm has been developed and implemented in two nodes COW system. Two typical EM simulation examples have been simulated. The results show good agreement between the GPU+COW scheme and the traditional CPU computing while at least 60 times speedup has been achieved.