In this paper, we propose a joint design of MIMO-PNC (multiple-input multiple-output physical layer network coding) and channel decoding in two way relay channels. The paper shows that if we adopt the same Repeat Accumulate (RA) channel code at the two end nodes, there would be a compatible decoder at the relay which can transform the received superimposed packet to the network coding form of the two packets efficiently. Specifically, we redesign the belief propagation decoding algorithm of the RA code for traditional point-to-point channel to suit the need of the MIMO PNC channel. The simulation results show that our new scheme outperforms the previously proposed schemes which combined MIMO NC with channel coding/decoding significantly in terms of BER with little added complexity.