In this work, we propose a pH-adjusted self-assembled lipid bilayer (LB) as signal output mode for the analysis of total N-glycolylneuraminic acids (TNeu5Gc) including free Neu5Gc and conjugated Neu5Gc. Based on synergistic inhibition effect of pH-adjusted self-assembled LB and TNeu5Gc on transport of hydrophilic probe, a ratiometric electrochemical biosensor has been elaborately constructed to decrease the experimental interferences and enhance analytical accuracy. The constructed biosensor has been successfully applied for electrochemical analysis of TNeu5Gc with a wide linear detection range from 2.816 ng/mL to 360.396 ng/mL and a low detection limit of 0.506 ng/mL. This work not only firstly establishes a ratiometric electrochemical biosensor for the analysis of TNeu5Gc, but also provides a new insight for self-assembly of LB in response to pH value change.