This paper presents a novel stimulus-response method for surface potential sensing of silicon nanowire (Si NW) field-effect transistors. When an "ion-step" from low to high ionic strength is given as a stimulus to the gate oxide surface, an increase of double layer capacitance is therefore expected. Thus, a change of conductance through the Si-NWs is measured. The surface potential on the Si-NW gate is changed from negative for a bare SiO2 surface to neutral/ positive when there is poly-L-lysine adsorption at certain pH, which also indicates a shift of point-of-zero charge pH after surface modification. This change is measured by a drop of current variation at the ion-step. The ion-step is performed to the Si-NW through a polydimethylsiloxane microfluidic chip with automatic sample switching. A reduction of the ion-step response from 2 nA to almost zero at pH 5.0 is observed by increasing the potassium ion concentration from 10 mM to 50 mM, which corresponds to a surface potential change of similar to 12 mV. We show that this method can be used as an alternative method for surface potential sensing, making it less sensitive to drift.