We developed a high spatially-resolved ion-imaging system using focused electron beam excitation. In this system, we designed a nanometric thin sensor substrate to improve spatial resolution. The principle of pH measurement is similar to that of a light-addressable potentiometric sensor (LAPS), however, here the focused electron beam is used as an excitation carrier instead of light. A Nernstian-like pH response with a pH sensitivity of 53.83 mV/pH and linearity of 96.15% was obtained. The spatial resolution of the imaging system was evaluated by applying a photoresist to the sensing surface of the ion-sensor substrate. A spatial resolution of 216 nm was obtained. We achieved a substantially higher spatial resolution than that reported in the LAPS systems.