Conventional lateral flow biosensing technologies face the dual formidable challenges of poor sensitivity and cumbersome quantitative devices. Here, we developed a Au@Pd nanopopcorn and aptamer nanoflower assisted lateral flow strip (ANAN-LFS) with a thermal signal output to improve detection sensitivity. Moreover, a smartphone-based thermal reader was designed and meticulously optimized to hand-held style, realizing the essential portability of this quantitative device. Experimental studies revealed that the synthesized Au@Pd nanopopcorns clearly red-shifted into the near-infrared region, thus resulting in a higher photothermal response than the standard gold nanoparticles. Aptamer nanoflowers enhanced the system's biorecognition ability significantly compared with single-stranded aptamers due to their functional spatial structure, thus resulting in an even greater improvement in the sensitivity of the ANAN-LFS. With exosomes as model targets, the limit of detection (LOD) was calculated to be 1.4 × 104 exosomes/μL, which exhibited a 71-fold improved analytical performance. The feasibility of this system for detecting spiked biological samples at clinical concentrations was also confirmed. These results suggest that the proposed strategy of integrating a ANAN-LFS with a smartphone-based thermal reader has great potential as a powerful tool for bioanalytical applications, offering the combined unique advantages of high sensitivity and expedient portability.