A linear precoding design scheme based on imperfect channel state information is proposed for multiple input multiple output MIMO twoway relay system with two communication nodes. This scheme considers the channel estimation error and feedback delay. The design of transceiver is simplified as an optimal problem with precoding matrix variables, which is deduced with the maximum power constraint at the relay station based on the minimum meansquare error criterion. With channel feedback delay at both ends of the channel and the channel estimation errors are taken into account, the matrix decomposition scheme and the joint iterative scheme are proposed to minimize the average sum meansquare error. Numerical simulation results show that the matrix decomposition scheme can improve the system bit error rate (BER) effectively and the joint iterative scheme achieves the best performance of BER with the increase of signaltonoise ratio against existing methods.