The single-atom dispersed active sites and the thicker catalytic layer of metal-nitrogen-carbon (M-N-C) electrocatalysts based membrane electrode assembly (MEA) exhibit notable distinctions from Pt-based MEA, necessitating targeted optimization. This study systematically investigates the influence of compression on both structure and performance of the M-N-C electrocatalysts based MEA. Four compression ratios, ranging from 11.5% to 39.3%, were examined across diverse operational conditions. The variations in impedance across different electrochemical regions are observed, resulting from the superposition of distinct impedance components. It is found that the insufficient compression leads to higher porosity and the formation of cracks between catalytic layer and membrane, adversely impacting internal resistance and proton transport. Increasing compression first acts the catalytic layer, and then gradually acts on the interface, membrane and gas diffusion layer, thereby reducing internal resistance, charge transfer resistances, albeit at the expense of heightened mass transfer resistance. Among these factors, the influence of internal resistance affects significance to total performance. Furthermore, compression influenced mass transfer differently in various layers. For the catalyst layer, the effect was uniform and sustained, while for the gas diffusion layer, it initially remained constant and then experienced a sudden deterioration over a certain extent. Optimal MEA performance is achieved when the compression ratio attains 40 %, which 2.1 times higher than the low compression MEA. This finding emphasizes the necessity for higher compression on M-N-C electrocatalysts based MEA compared to Pt-based MEA.