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Partial decoding has the potential to achieve a larger capacity region than full decoding in two-way relay (TWR) channels. Existing partial decoding realizations are however designed for Gaussian channels and with a static physical layer network coding (PLNC). In this paper, we propose a new solution for joint network coding and channel decoding at the relay, called pairwise check decoding (PCD), for low-density parity-check (LDPC) coded TWR system over block fading channels. The main idea is to form a check relationship table (check-relation-tab) for the superimposed LDPC coded packet pair in the multiple access (MA) phase in conjunction with an adaptive PLNC mapping in the broadcast (BC) phase. Using PCD, we then present a partial decoding method, two-stage closest-neighbor clustering with PCD (TS-CNC-PCD), with the aim of minimizing the worst pairwise error probability. Moreover, we propose the minimum correlation optimization (MCO) for selecting the better check-relation-tabs. Simulation results confirm that the proposed TS-CNC-PCD offers a sizable gain over the conventional XOR with belief propagation (BP) in fading channels.