Molecular imaging techniques based on surface-enhanced Raman scattering (SERS) face a lack of reproducibility and reliability, thus hampering its practical application. Flower-like gold nanoparticles have strong SERS enhancement performance due to having plenty of hot-spots on their surfaces, and this enhancement is not dependent on the aggregation of the particles. These features make this kind of particle an ideal SERS substrate to improve the reproducibility in SERS imaging. Here, the SERS properties of individual flower-like gold nanoparticles are systematically investigated. The measurements reveal that the enhancement of a single gold nanoparticle is independent of the polarization of the excitation laser with an enhancement factor as high as 108. After capping with Raman signal molecules and folic acid, the gold nanoflowers show strong Raman signal in the living cells, excellent targeting properties, and a high signal-to-noise ratio for SERS imaging.