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Cooperative relay networks combined with Orthogonal Frequency Division Multiplexing Access (OFDMA) technology has been widely recognized as a promising candidate for future cellular infrastructure due to the performance enhancement by flexible resource allocation schemes. The majority of the existing schemes aim to optimize single cell performance gain. However, the higher frequency reuse factor and smaller cell size requirement lead to severe inter-cell interference problem. Therefore, the multi-cell resource allocation of subcarrier, time scheduling and power should be jointly considered to alleviate the severe inter-cell interference problem. In this paper, the joint resource allocation problem is formulated. Considering the high complexity of the optimal solution, a two-stage resource allocation scheme is proposed. In the first stage, all of the users in each cell are selected sequentially and the joint subcarrier allocation and scheduling is conducted for the selected users without considering the interference. In the second stage, the optimal power control is performed by geometric programming method. Simulation results show that the proposed the interference-aware resource allocation scheme improves the system capacity compared with existing schemes. Especially, the edge users achieve more benefit.