With the development of the shipbuilding industry, it is necessary to improve tribological properties of polyether ether ketone (PEEK) as a water-lubricated bearing material. In this study, the sulfonated PEEK (SPEEK) with three distinct chemical structures was synthesized through direct sulfonated polymerization, and high fault tolerance and a controllable sulfonation degree ensured the batch stability. The tribological and mechanical properties of SPEEK with varying side groups (methyl and tert-butyl) and rigid segments (biphenyl) were compared after sintering in a vacuum furnace. Compared to the as-made PEEK, as the highly electronegative sulfonic acid group enhanced the hydration lubrication, the friction coefficient and wear rate of SPEEK were significantly reduced by 30% and 50% at least without affecting the mechanical properties. And lower steric hindrance and entanglement between molecular chains were proposed to be partially responsible for the lowest friction behavior of SPEEK with methyl side groups, making it a promising and competitive option for water-lubricated bearings.