In this work, we measured the time evolution of the transmission features of 10-100 keV protons transmitted through nanocapillaries in a polycarbonate (PC) membrane. After reaching equilibrium, transmitted particles with an incident energy of 100 keV were located around the direction along the incident beam but not along the capillary axis, indicating that the transport mechanism of the 100 keV ion was distinct from that of keV-energy ions. The simulation results indicated that charge-patch-assisted collective scatterings on the surface are the main transport mechanism for the hundred-keV ions in nanocapillaries. This scenario fills in the gap in the previous understanding of ion transmission in nanocapillaries from keV to MeV energies.