Aptamers, with numerous advantages over antibodies, such as high stability, resistance to denaturation and degradation, and easy modification possibilities, have found widespread uses in biosensing, drug delivery, disease diagnosis and therapy. The specific binding ability of aptamers to cancer-related markers and cancer cells ensured high performance for early diagnosis of cancer. Carcinoembryonic antigen (CEA) usually is present only at very low levels in the blood of healthy adults, however, the levels can raise in certain kinds of cancers such as colon and rectal cancer, pancreas, breast, ovary or lung cancer, allowing CEA to be used as a tumor marker in clinical tests. Several research groups have further demonstrated the levels of CEA are significantly higher in saliva than in blood/serum. Here, we present an aptamer-based biosensor for CEA’s detection with a sensitivity of 0.399 µA/(ng/mL) in saliva. The binding affinities of the selected aptamers to CEA have been evaluated by Surface Plasmon Resonance imaging (SPRi) technology which is a very sensitive method to measure binding interactions of various biomolecules, including proteins, nucleic acids, and phospholipids. Furthermore, instead of using the time-consuming Systematic Evolution of Ligands by Exponential enrichment (SELEX) process, we proposed a molecular dynamics (MD) simulation method to automatically and effectively select target-specific aptamers. It systematically investigates the atomistic details of the binding mechanisms between aptamer and target. Complemented with experimental tests, SPRi validation and MD simulation, this electrochemical aptamer-based biosensing system demonstrates great sensitivity, clinically accuracy and reliability in realizing noninvasive disease detection and monitoring through saliva analysis.