In this study, highly uniform 3D Al nanoneedle arrays (AlNNAs) decorated with Ag nanopines are synthesized by anodization of Al foil with prior nanoimprinting and subsequent electrodeposition method, demonstrating remarkable surface-enhanced Raman scattering (SERS) property. The AlNNAs possess a highly ordered periodicity of 1 μm and nanoneedle height of 800 nm, making it an optimal supporting matrix to host Ag-NPs as SERS substrate. Such well-ordered Ag@AlNNAs SERS substrate with precisely electrodeposited Ag nanopines generate high density SERS host spots and abundant sites to adsorb target molecules. As a result, Ag@AlNNAs exhibit high sensitivity for rhodamine 6 G down to 10–13 M and good signal reproducibility with a relative standard deviation of 7.2 %, as well as an average enhancement factor of 4.23 × 109. For practical detection of pollutants, 10–8 M adenine, 10–12 M bisphenol in water, and melamine (10–7 M) in opaque milk are clearly identified by using the Ag@AlNNAs sensor. This study opens a bright way to fabricate SERS substrate with a good balance of sensitivity, reproducibility and cost, indicating promising potential for environmental monitoring and food safety.