Instead of the canonical Grotthuss mechanism, we show that a knock-on proton transport process is preferred between organic functional groups (e.g., -COOH and -OH) and adjacent water molecules in biological proton channel and synthetic nanopores through comprehensive quantum and classical molecular dynamics simulations. The knock-on process is accomplished by the switching of covalent O─H bonds of the functional group under externally applied electric fields. The proton transport through the synthetic nanopore exhibits nonlinear current-voltage characteristics, suggesting an unprecedented proton Coulomb blockade effect. These findings not only enhance the understanding of proton transport in nanoconfined systems but also pave the way for the design of a variety of proton-based nanofluidic devices.