Against the global low-carbon transition drive, mudstone biogas represents a vital unconventional natural gas resource. Yet unclear micro-scale gas-displacing-water mechanisms hinder its productive exploitation. This work combines multi-pressure NMR displacement tests and mono-multifractal coupling analysis to quantify dynamic pore evolution, overcoming limits of conventional static pore characterization. Mudstone core samples from the Sanhu area of Qaidam Basin are analyzed to decode biogas charging controls and build a multi-factor coupling model. Results reveal that micro–mesopores dominate reservoirs; brittle minerals form rigid pore frameworks, while water-wet clays impede gas flow. Gas–water displacement proceeds in staged preferential flow, with two threshold pressures (8 MPa, 15 MPa) slowing efficiency gains. Fractal indices reliably reflect gas–water partitioning. Pore geometry and mineral assemblages jointly govern biogas accumulation; intervals with well-connected pores, weak water wettability and low clay content favor gas charging. The findings support the exploration of analogous continental mudstone gas reservoirs.