Metallo-dielectric photonic crystals (MDPCs) are used as ultrasensitive molecular detectors for concentrations down to picomolar level based on surface-enhanced Raman spectroscopy (SERS). Calculations show that the amorphous silicon photonic crystals (a-Si PCs) embedded in multiple metallo-dielectric (MD) units can significantly increase the electromagnetic fields at the air-dielectric interface, leading to remarkable Raman enhancement. Corresponding experiments show the multiple MDPC structures can serve as an ultrasensitive SERS substrate with excellent reproducibility and stability, capable of quantitative analysis down to 10 pM level. The MDPC structure can be generalized to other applications, such as plasmonic devices, ultrasensitive sensors, and nanophotonic systems.