Herein, we developed a natural surface-enhanced Raman scattering (SERS) substrate based on size-tunable Au@Ag nanoparticle-coated mussel shell to form large-scale three-dimensional (3D) supercrystals (up to 10 cm2) that exhibit surface-laminated structures and crossed nanoplates and nanochannels. The high content of CaCO3 in the mussel shell results in superior hydrophobicity for analyte enrichment, and the crossed nanoplates and nanochannels provided rich SERS hot spots, which together lead to high sensitivity. Finite-difference time-domain simulations showed that nanoparticles in the channels exhibit apparently a higher electromagnetic field enhancement than nanoparticles on the platelets. Thus, under optimized conditions (using Au@AgNPs with 5 nm shell thickness), highly sensitive SERS detection with a detection limit as low as 10-9 M for rhodamine 6G was obtained. Moreover, the maximum electromagnetic field enhancement of different types of 3D supercrystals shows no apparent difference, and Au@AgNPs were uniformly distributed such that reproducible SERS measurements with a 6.5% variation (613 cm-1 peak) over 20 spectra were achieved. More importantly, the as-prepared SERS substrates can be utilized for the fast discrimination of Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa by discriminant analysis. This novel Au@Ag self-assembled mussel shell template holds considerable promise as low-cost, durable, sensitive, and reproducible substrates for future SERS-based biosensors.