The development of rapid and ultra-sensitive aptamer-based lateral flow assay (Apt-LFA) for the detection of small molecules remains a significant challenge. In this study, we developed a colorimetric-photothermal "turn on" mode LFA for detecting tetrodotoxin (TTX) by integrating magnetic polyvalent aptamers (MB@poly-Apts) and onion flower-like gold-palladium nanoparticles (MOGP). Guided by structural information of the aptamer, we employed a truncation optimization strategy to rationally develop the TTX-specific aptamer A36. The capture probe, MB@poly-Apts, was synthesized by modifying magnetic beads with a rigid DNA linker, the truncated aptamer A36, and a complementary linker. This poly-Apts exhibited an enhanced binding affinity (9.3 nM) by 4-fold and binding efficiency by 2-fold for TTX attributed to its unique design featuring polyvalent binding sites and gaps in the complementary structure. The signaling probe, MOGP, possessed a broad absorption spectrum, a multibranched structure, and bimetallic/polydopamine compositions, providing excellent colorimetric properties, catalytic activity, and photothermal performance. The developed MB@poly-Apts-assisted MOGP-based LFA achieved colorimetric, catalytically enhanced colorimetric, and photothermal modes of TTX detection with visual detection limits as low as 1, 0.01, and 0.025 ng/mL, respectively. This performance significantly outperforming traditional gold nanoparticle-based LFA. The Apt-LFA demonstrated ultra-sensitivity with good flexibility, positioning it as a promising platform for on-site testing for diverse applications.