Metal-organic frameworks (MOFs)-doped hybrid SPAEK-based proton exchange membranes (PEMs) can combine the advantages of both to promote the comprehensive performance of hybrid membranes. However, the complicated preparation process and low yield of functionalized MOF restricted their application in organic-inorganic hybrid PEMs. Herein, an amino-sulfonic acid-based bi-functionalized MOF (MNCS), containing flexible sulfonic acid chains, was prepared by an uncomplicated and efficient one-step modification method. The sulfonic acid groups on MNCS were grafted to the end of flexible side chains with large free volume, which facilitated the formation of broad and continuous proton transport channels to reduce the activation energy of proton transport. Meanwhile, the amino groups of MNCS establish a second proton transport channel with the sulfonic acid groups in SPAEK due to acid-base pair interactions. Furthermore, owing to the formation of the ionic cross-linking structure, the dimensional stability and methanol resistance of MNCS@SNF-PAEK were significantly improved. Especially, MNCS@SNF-PAEK-1.5 showed the highest proton conductivity of 0.188 S cm−1,endowing it with a maximum power density of 90.8 mW cm−2 in direct methanol fuel cell (DMFC), which substantially exceeded that of pristine SNF-PAEK membrane. It illustrated that the hybrid membranes by incorporating MNCS showed promising potential in DMFC.