In this article, the comparative study of surface-enhanced Raman scattering (SERS) performance of assembled Au nanorods (AuNRs) and Au nanodumbbells (AuNDs) based on capillaries was introduced. Under the same conditions of the synthetic precursor and the dispersed system, two kinds of nano units were assembled on the inner wall of capillaries based on the same surface ligand exchange treatment process and the same assembly technology. And the AuNDs assembly structures based on capillary (AuNDs/cap) showed more significant SERS activity. Meanwhile, the uniform and reproducibility of the two assembly structures were pretty much the same. Furthermore, the AuNDs/cap structures can be used for sampling and SERS detection of malachite green (MG) down to 2×10-3μg/g levels in real water samples, which exhibit an excellent practicability and a great promise for rapid and credible practical detection.