To detect biochemicals with ultra-high sensitivity, efficiency, reproducibility and specificity has been the Holy Grail in the development of nanosensors. In this work, we report an innovative type of photonic-plasmonic hybrid Raman nanosensors integrated with electrokinetic manipulation by rational design, which offers dual mechanisms that enhance the sensitivity for molecule detection directly in solution. For the first time, we integrate large arrays of synthesized plasmonic nanocapsules with densely surface distributed silver (Ag) nanoparticles (NPs) on lithographically patterned photonic crystals via electric-field assembling. With the patterned microelectrodes, the applied electric fields not only assemble the hybrid plasmonic nanocapsules on photonic crystals but also generate electrokinetic flows that focus analyte molecules to the Ag hot spots on the nanocapsules for Surface-enhanced Raman scattering (SERS) detection. The synergistic effects of plasmonic-photonic resonance and the electrokinetic molecular focusing can promote the SERS enhancement factor (EF) robustly to 5×10⁹- 5×10¹⁰. Various molecules including SERS probing molecules, nucleobases, and unsafe food additives can be detected directly from suspension. The innovative mechanism, design, and fabrication reported in this work can inspire a new paradigm for achieving high-performance Raman nanosensors, which is pivotal for lab-on-chip disease diagnosis and environmental protection.