Hydrogen-air proton exchange membrane fuel cells (PEMFCs) and direct methanol fuel cells (DMFCs) are excellent fuel cells with high limits of energy density. However, the low carbon monoxide (CO) tolerance of the Pt electrode catalyst in hydrogen-air PEMFCs and methanol permanent in DMFCs greatly hindered their extensive use. Applying polybenzimidazole (PBI) membranes can avoid these problems. The high thermal stability allows PBI membranes to work at elevated temperatures when the CO tolerance can be significantly improved; the excellent methanol resistance also makes it suitable for DMFCs. However, the poor proton conductivity of pristine PBI makes it hard to be directly applied in fuel cells. In the past decades, researchers have made great efforts to promote the proton conductivity of PBI membranes, and various effective modification methods have been proposed. To provide engineers and researchers with a basis to further promote the properties of fuel cells with PBI membranes, this paper reviews critical researches on the modification of PBI membranes in both hydrogen-air PEMFCs and DMFCs aiming at promoting the proton conductivity. The modification methods have been classified and the obtained properties have been included. A guide for designing modifications on PBI membranes for high-performance fuel cells is provided.