For completion of on-chip field effect transistor (FET) biosensors, it is essential to produce a reference FET instead of a reference electrode that uses an inner electrolyte. In this study, a light-addressable potentiometric sensor (LAPS) modified by a self-assembled monolayer (SAM) of octadecylsilane (ODS) was pH-insensitive (-1.5 mV/pH), but it was sensitive to ionic strength as was reported in polymer-gate FETs. Our purpose was to make clear the problems of the evaluation methods of ODS-SAM FETs concerning pH and ionic responses and the effect of the surface morphology to improve a reference SAM-FET. An ODS-SAM LAPS and FET were deposited under different conditions. pH and ionic responses, roughness measured by atomic force microscope, and contact angle (CA) were greatly changed by the difference in morphology of the ODS-SAM. ODS coagulation raised the CA. It is difficult to distinguish the ODS-SAM with and without ODS coagulation only by CA, but CA is utilizable for observing the state of hydroxyl groups on the surface without ODS coagulation. ODS coagulation caused the pH response with the ODS-SAM but decreased the ionic response of the LAPS. Controlling the surface morphology of the ODS-SAM is important to suppress the pH and ionic sensitivities for an in vivo applicable reference FET.