Enhancing the proton conductivity of proton exchange membranes (PEMs) is essential to expand the applications of proton exchange membrane fuel cells (PEMFCs). Inspired by the proton conduction mechanism of bacteriorhodopsin, cucurbit[n]urils (CB[n], where n is the number of glycoluril units, n = 6, 7, or 8) are introduced into sulfonated poly(ether ether ketone) (SPEEK) matrix to fabricate hybrid PEMs, employing a nature-inspired chemical engineering (NICE) methodology. The carbonyl groups of CB[n] act as proton-conducting sites, while the host–guest interaction between CB[n] and water molecules offers extra proton-conducting pathways. Additionally, the molecular size of CB[n] aids in their dispersion within the SPEEK matrix, effectively bridging the unconnected proton-conducting sulfonic group domains within the SPEEK membrane. Consequently, all hybrid membranes exhibit significantly enhanced proton conductivity. Notably, the SPEEK membrane incorporating 1 wt.% CB[8] (CB[8]/SPEEK-1%) demonstrates the highest proton conductivity of 198.0 mS·cm⁻¹ at 60 °C and 100% relative humidity (RH), which is 228% greater than that of the pure SPEEK membrane under the same conditions. Moreover, hybrid membranes exhibit superior fuel cell performance. The CB[8]/SPEEK-1% membrane achieves a maximum power density of 214 mW·cm⁻², representing a 140% improvement over the pure SPEEK membrane (89 mW·cm⁻²) at 50 °C and 100% RH. These findings serve as a foundation for constructing continuous proton-conducting pathways within membranes by utilizing supramolecular macrocycles as fuel cell electrolytes and in other applications.