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• A SMA-SERS was obtained with the combination of laser microfabrication and sputtering. • A SMA-SERS is hierarchically ordered and assembled from plasmonic nanoparticle clusters. • The detection of trance amount of R6G molecules is achieved using such a SMA-SERS. • The sensitivity is affected by laser pulse number, film thickness and the microcrater. Surface-enhanced Raman scattering (SERS) with unique molecular vibrational fingerprints for identifying analytes provides an effective spectroscopic approach for the detection of trace molecules in biomedical/analytical fields. Although a great amount of efforts has been devoted to developing various SERS substrates with hierarchical micro/nanostructures, challenges remain in completely concentrating the target molecules within a sensitive area and thereby enhancing detection sensitivity. Here, we report trace molecular detection using superhydrophobic microcrater array as surface-enhanced Raman substrate (SMA-SERS). The hierarchically ordered microcrater array with plasmonic nanoparticle clusters is quickly obtained by the two-step process of femtosecond laser texturing and magnetron sputtering. The resultant substrates with hierarchical micro-/nanostructures show excellent superhydrophobicity with a contact angle above 150° and satisfactory plasmonic nanostructures with the easily attainable Raman signal enhancement factor of ~4.82 × 108. The signals on the SMA-SERS maintain uniformity with a relative standard deviation of <15%. These findings manifest that the SMA-SERS is an extraordinary strong candidate for obtaining high-quality and reliable SERS, facilitating a widespread use of SERS for practical applications. [ABSTRACT FROM AUTHOR]