Relay technique is introduced in the Long Term Evolution Advanced (LTE-Advanced) system to extend the network coverage, improve the performance of cell-edge user equipments (UEs) and increase the fairness among different UEs. The combination of multiple-input-multiple-output (MIMO) and relay can further increase frequency efficiency and improve system performance. In this paper, based on the architecture of MIMO relay-enhanced TD-LTE-Advanced system, a fairness -aware resource allocation algorithm is proposed, and the resource allocation is divided into 3 phases: a frequency resource partition scheme is firstly proposed to realize the tradeoff between fairness among UEs served by various relay nodes and system throughput; and secondly, a backhaul resource allocation algorithm is presented to match the eNB to relay transmission with the relay to UE transmission with reduced feedback overhead; finally, a resource allocation algorithm from eNB and relay to UEs is given to maximize the proportional fairness so that user fairness can be guaranteed. The property of the proposed resource allocation algorithm is investigated through system level simulation and the results show that both system throughput and user fairness can be improved with limited feedback overhead, compared with the existing algorithms.