Molecularly imprinted electrochemical sensor is a kind of convenient, fast, and stable analyzer, but the conductivity of electrode materials and their affinity with the analyte affect its performance. A proton acid (PSS, SA, SSA) doping method was proposed to improve the electrochemical performance of the polypyrrole molecularly imprinted polymer (PPy-MIP), which promoted the electropolymerization of pyrrole, reduced the charge transfer resistance, and increased the electrochemical surface area. In terms of both improving conductivity and affinity, the response of the proton acids doped the polypyrrole molecularly imprinted electrochemical sensors (PPy-MIECS) to urea was improved by 25-fold (PSS), 5-fold (SA), and 3-fold (SSA) over that of PPy-MIECS. In addition, the PSS-PPy-MIECS was validated for the practical application with a linear detection range from 0.1 mM to 100 mM, high selectivity (α = 39.73), reusability (RSD% = 4.54 %), reproducibility (RSD% = 0.93 %), and stability (11 days). The advantage of proton acid doping method in PSS-PEDOT-MIECS to urea and PSS-PPy-MIECS to glucose extended its application in the performance enhancement of MIECS design.