The detection rate of Salmonella in raw eggs is as high as 3.9%~43.7%. To achieve sensitive, rapid, and accurate detection of Salmonella in raw eggs, this study aimed to investigate the performance differences of various aptamer sequences in electrochemical sensors and construct an efficient electrochemical aptamer-based sensor. Based on four previously reported Salmonella aptamer sequences, this study first compared their recognition capabilities and affinities for Salmonella in electrochemical sensors, identifying the optimal aptamer sequence. Subsequently, an electrochemical aptamer-based sensor was constructed using this sequence, and its linear range, detection limit, reproducibility, specificity, and spike recovery rate in actual samples then evaluated. The results demonstrated that Aptamer Sequence 1 exhibited the strongest recognition capability and affinity in the electrochemical sensor. The sensor constructed based on this sequence showed a linear range of 3.37~3.37×107 CFU/mL, a detection limit of 1 CFU/mL (S/N=3), and excellent reproducibility and specificity. The spike recovery rate in raw egg samples ranged from 81.51~109.35%. This study provides a theoretical basis for the selection of aptamers in electrochemical sensors and successfully developed a rapid and accurate electrochemical aptamer-based sensor for detecting Salmonella in raw eggs, offering new technical support for food safety detection.