Morphological control is essential for tuning the performance of polymer electrolyte membranes (PEMs). Block copolymerization is an effective but complicated way to control the morphology of PEMs. It is urgent to explore a simple alternative method to achieve this target. Herein, the molecular engineering strategy that changes the molecular structure and volume of hydrophobic cross-linkable diamine and introduces a hydrophobic network structure was used to optimize the microphase morphology of sulfonated polyimides (SPIs). Three diamine monomers containing tetrafluorostyrol pendant groups have been synthesized (4-(2,3,5,6-tetrafluoro-4-vinylphenoxy)benzene-1,3-diamine (TFVPDM), 1,3-bis(2-trifluoromethyl-4-amino-phenoxy)-5-(2,3,5,6-tetrafluoro-4-vinylphenoxy)benzene (6FTFPB), 2,2-bis(3-amino-4-(2,3,5,6-tetrafluoro-4-vinylphenoxy)phenyl)hexafluoropropane (6FATFVP)). Based on these monomers, 4,4′-diaminostilbene-2,2′-disulfonic acid (DASDSA) and 1,4,5,8-naphthalenetetracarboxylicdianhydride (NTDA), three cross-linked SPIs (CSPIs: CSPI-T-10, CSPI-TP-10, CSPI-AP-10) with similar ion-exchange capacity (IEC) value of 2.29–2.46 meq. g−1 but different main-chain structures were prepared through polycondensation and thermal cross-linking process. The introduced hydrophobic cross-linked structure improves the oxidative stability and methanol resistance of CSPI membranes. The CSPI membranes prepared from cross-linkable hydrophobic diamine with larger molecular volume and containing hydrophobic structural units in the main chain exhibit more pronounced phase separation morphology and higher proton conductivity. Moreover, the methanol resistance of CSPI membranes is dependent on the combined effect of IEC, degree of crosslinking (DC), and main-chain structure. The higher DC and main-chain containing hydrophobic structure are beneficial for enhancing the methanol resistance. The CSPI-AP-10, which was prepared from the 6FATFVP with the largest molecular volume, more hydrophobic cross-linkable pendant groups and hydrophobic linkages, exhibits the best performance. The CSPI-AP-10 membranes showed high proton conductivity and excellent methanol resistance. The direct methanol fuel cells (DMFCs) assembled from CSPI-AP-10 have a high max power density (PDmax) of 106.2 mW cm−2 in 2 M methanol and 75.1 mW cm−2 in 10 M methanol. The results indicated that the CSPI-AP-10 was a promising candidate as a PEM in DMFC application.
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