In this study, composite proton exchange membranes (PEMs) based on functional graphene oxide (GO) and carboxyl-containing sulfonated poly(arylene ether ketone sulfone)s organic matrix (C-SPAEKS) were synthesized. Modified GO nanosheets (ATP@GO) was synthesized by using GO as a template, then chemically bonded adenosine triphosphate (ATP) on GO nanosheets. Modified ATP@GO and composite membranes were characterized by FT-IR, 1H NMR, SEM and XPS. These composite membranes exhibit outstanding proton conductivity, thermal stability and dimensional stability. Compared to C-SPAEKS membranes (32.3 mS cm−1 at 20 °C, 108.9 mS cm−1 at 90 °C), C-SPAEKS/ATP@GO-1 membrane showed enhanced proton conductivity (50.0 mS cm−1 at 20 °C, 184.8 mS cm−1 at 90 °C). Meanwhile, the open circuit voltage (OCV) and power density of C-SPAEKS/ATP@GO-1 were 0.9941 V and 466.33 mW/cm2, respectively, which were much higher than the C-SPAEKS (0.8973 V, 190.72 mW/cm2), showing good fuel cell performance. The results show that functionalized GO could make an important contribution to proton conduction and improvement of comprehensive performance in composite membrane, which indicate that these composite membranes have the potential to be used as PEMs.