The prevalence and significant health risks associated with mycotoxin contamination in traditional Chinese medicines underscore the need for on-site detection methods. The complexity of matrices necessitates sample pretreatment before analysis, leading to prolonged analysis times and intricate procedures. In this study, we employed aptamer-modified magnetic nanoparticles (aptamer-MNPs) as labels and devised a three-in-one lateral flow aptasensor for on-site detection of ochratoxin A (OTA) in Astragalus membranaceus. By integrating aptamer-MNPs that serve in recognition, separation, and signal amplification roles, we streamlined purification, enrichment, and detection within a single aptasensor in 30 minutes. The developed aptasensor demonstrated high sensitivity (0.053 ng/mL), excellent specificity, and satisfactory accuracy. Analyzing twelve actual samples revealed three as OTA-positive, aligning well with HPLC analysis results. These results showcase the potential of the lateral flow aptasensor as a cost-effective, reliable, and robust on-site screening technique for trace-level mycotoxins in complex matrices.