This paper focused on the complementary advantages of density functional theory (DFT) calculation and catalytic reaction regulation. Based on the effective identification of intermediates, the possible catalytic hydroconversion (CHC) pathways of lignite-derived aryl ethers over Ni/mordenite were discussed. Bond dissociation energy (BDE) calculations of >C–O– bonds in different substrates and intermediates show that BDEs of >Car–O– bonds are generally higher than those of >Cal–O– bonds, and there is obvious electron aggregation near O atoms. Mulliken charge distribution analyses of different atomic sites further revealed the possible adsorption sites of active hydrogen, especially H· and H+. Possible cleavage pathways were further speculated by evaluating the stability of different leaving groups. In the early stage of CHC, aromatic ring hydrogenation and >Cal–O– bond cleavage dominate, rather than >Car–O– bond cleavage. Enthalpy change analyses combined with the CHC of real substrates further indicate that lowering temperature is beneficial to the cleavage of >Car–O– bonds under the premise of inhibiting H···H transfer and obtaining H· effectively. Appropriately increasing the support acidity to ensure sufficient H+ release is conducive to >Cal–O– bond cleavage, especially direct dehydroxylation/dehydration. The analysis of synergetic transfer pathways of active hydrogen during the CHC provides theoretical guidance for the pathway optimization of converting lignite into high-quality clean liquid fuels.