In this paper, we study the problem of joint resource allocation in the two-way relay system, where a pair of multi-antenna users wish to exchange information via multi-antenna amplify-and-forward relay under orthogonal frequency-division multiplexing (OFDM) modulation. We formulate a sum-rate maximization problem subject to a limited power constraint for each user and relay. Our resource allocation strategy aims at finding the best pairing scheme and optimal power allocation over subchannels in frequency and space domains. This turns out to be a mixed integer programming problem. We then derive an asymptotically optimal solution though the Lagrange dual decomposition approach. Finally, simulation results are provided to demonstrate the performance gain of the proposed algorithms.