High-ordered particle-in-bowl (PIB) arrays are developed in this paper for surface enhanced Raman spectroscopy (SERS). A heterogeneous shadow mask, composing of the chrome (Cr) layer and colloid residues, is used to fabricate the silicon ( Si ) template from where the PIB arrays finally lift-off. The finite difference time domain (FDTD) method is employed to investigate the Raman enhancement mechanism of this PIB architecture. The electromagnetic (EM) field tends to concentrate in the gap between the bowl and the particle forming the "hot spots". The enhancement factor (EF) of the EM field is about 70 with an excitation wavelength of 785 nm. The Raman measurements validate the EM calculation of the PIB arrays. The EF is about 1.12 × 107 using Rodamine 6G (R6G) as probe molecule. The proposed PIB array is high-ordered in morphology and ultra-sensitive in Raman measurement, providing an ideal substrate for SERS-based bio-chemical sensing, disease diagnosis and analytical chemistry.