A simple and quick electrochemical sensor has been developed for the detection of saxitoxin (STX) based on the specific peptides, which were screened and identified by molecular simulation and electrochemical characterization, respectively. The library of saxitoxin peptides was obtained followed by structural analysis of the receptor and STX, molecular docking, amino acid mutation, and molecular dynamics. The specific peptide (named S4) was screened by the theoretical interaction energy (ΔE) and the fact electrochemical identification. Meanwhile, the reduced graphene oxide (rGO) and gold nanoparticles (AuNPs) materials were introduced to improve the electron mass transfer and increase the electrochemical signal. Under the optimal condition, one simple and quick electrochemical sensor was developed between the ΔI and the concentration of STX in the range of 10 ∼ 1000 ng/L with a limit of detection (LOD) of 6.9 × 10–4 μg/L (S/N = 3). In seawater, artificial seawater, and oyster powder samples, a good recovery rate was found in the range of 87.3 %–116.2 %. In addition, excellent selectivity, good reproducibility, and stability were obtained. It provides a novel idea for the screening of the specific peptides of toxins and the development of the electrochemical peptides sensor.