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This letter addresses the joint linear processing issues for 3-phase two way cooperative MIMO relay systems, aiming to minimize the mean squared error (MMSE). Considering the difficulty to acquire the channel state information (CSI) of the direct link at relay node, we first derive an iterative linear processing scheme for the relay node ignoring the direct link between two source nodes. Then the receive processing matrix combining the signal from direct link and relay link can be easily given according to MMSE orthogonality principle. Finally by comparing other schemes that can accomplish bidirectional data exchange, simulation results show that our proposed 3-phase cooperative scheme can achieve better tradeoff of link reliability and spectrum efficiency especially when the direct link is in medium quality.