How to fabricate Au nanostructures conveniently on microstructured/nanostructured arrays surface with low cost has become a crucial and urgent challenge. In this study, we demonstrate hierarchical flowerlike Au nanostructures with rich nanothorns (HF-AuNTs) through one-step electrochemical deposition. The morphology of the HF-AuNTs is easily manipulated by controlling the applied potential or precursor solution concentration of electrodeposition. The as-prepared HF-AuNTs possessing unique local morphology of thin petals and dense thorns are further applied in the Si micropit arrays to acquire HF-AuNTs microarrays. As an initial detection, these HF-AuNTs microarrays exhibit a fascinating surface-enhanced Raman spectroscopy consistency (relative standard deviation is 7.17%) and sensitivity with the limitation of crystal violet reaching to 10-10 M, and Rhodamine 6G reaching to 10-11 M. The HF-AuNTs microarrays with well-defined shape and elaborate structure may be applicated in SERS substrates, superhydrophobic materials, and so on.