To investigate the effect of different stimulation modes on cortical electrically evoked potentials (EEPs) by intraorbital optic nerve (ON) stimulation with penetrating electrodes. A stimulating electrode array with three electrodes arranged linearly was inserted into the ON along its axis. EEPs were recorded using a 4 × 4 silver-ball electrode array in response to monopolar and bipolar stimulation mode, respectively. The simultaneous monopolar stimulation mode had a lower threshold than the individual monopolar stimulation mode, but elicited smaller cortical response when a fixed charge was injected. The threshold of the bipolar stimulation mode was comparable to that of individual monopolar stimulation mode. The response to the smaller spacing (150μm) bipolar stimulation mode was similar in amplitude to that of the individual monopolar stimulation mode, but spread wider. The larger spacing (500μm) bipolar stimulation mode elicited stronger and wider response than the individual monopolar stimulation mode. For the individual monopolar stimulation mode, stimulation with different electrodes can be differentiated even when the spacing of the two electrodes was 150μm. For ON stimulation with penetrating electrodes, the monopolar stimulation mode could induce more localized cortical responses than the bipolar stimulation mode with comparable threshold and had a high stimulation selectivity. These findings may provide valuable information for the design of stimulation strategy of the penetrative ON visual prosthesis.