Covalent organic frameworks (COFs) have emerged as promising substrates for surface-enhanced Raman scattering (SERS) due to their highly ordered crystalline porous architecture, superior molecular adsorption and enrichment capabilities, and excellent thermal and chemical stability. However, pure COFs inherently lack plasmonic resonance and free electron density, resulting in limited electromagnetic enhancement and overall weak SERS signal, which hinders their practicality in ultrasensitive molecular detection applications. To overcome these limitations, this study aims to design and synthesize a novel ruthenium-based covalent organic framework composite (Ru-COF) by integrating ruthenium complexes directly into the COF skeleton, thereby creating a metal-organic, synergy-enhanced SERS substrate suited for trace analysis in real water. A Ru-COF is synthesized by solvothermal condensation of 1, 2, 4, 5-benzenetetramine (BTA·4HCl) with tris (4, 4'-dicarboxy-2, 2'-bipyridyl) ruthenium, forming Ru-N/O coordinated nodes within the framework. The material is characterizedusing X-ray diffraction (XRD) to confirm enhanced π-π stacking and new crystalline peaks at 10.2° and 16° in Ru-COF, Fourier-transform infrared spectroscopy (FT-IR) to verify amide and benzimidazole bond formations with shifts indicating Ru integration, Brunauer-Emmett-Teller (BET) analysis to reveal the increased specific surface areas (22.5 m²/g for Ru-COF vs. 17.2 m²/g for COF), and scanning electron microscopy (SEM) with energy-dispersive X-ray spectroscopy (EDS) mapping to show uniform distribution of C, N, O, and Ru elements in a dense layered morphology. SERS performance is evaluated using methylene blue (MB) as a probe molecule on a Renishaw InVia Raman spectrometer (514.5 nm excitation, 40 mW power, 10 s exposure), with additional tests on 4-mercaptobenzoic acid (4-MBA) for universality assessment. Enhancement mechanisms are analyzed through energy level alignments, with Ru-COF’s HOMO/LUMO at –0.95 eV/–1.12 eV (vs. vacuum) facilitating hole-injection charge transfer to MB’s levels (–2.34 eV/–4.15 eV), enhancing polarizability derivatives and Raman cross-sections via Herzberg-Teller coupling. The results demonstrate that Ru-COF exhibits superior SERS activity compared with pure COF and Ag-COF. For MB detection, the characteristic peak at 1624 cm^–1 shows an analytical enhancement factor (EF) of 1.83 × 10¹⁰, calculated from normalized intensities and molecular densities, which far exceeds COF’s performance. Concentration-dependent spectra reveal a linear response from 10^–3 to 10^–13 mol/L (R² = 0.997), with a limit of detection (LOD, S/N = 3) of 4.16 × 10^–12 mol/L. Signal reproducibility is excellent, with a relative standard deviation (RSD) of 3.41% across 10 random spots. Cycling tests (5 repetitions) retain 90.2% of initial intensity, and long-term stability assessment shows 85.7% signal retention after four-months of air exposure. For 4-MBA, non-resonant enhancement yields an LOD of 10^–12 mol/L, dominated by CM via interfacial coordination and π-π interactions. In complex matrices such as tap and river water, Ru-COF maintains LODs of 5.2 × 10^–12 mol/L and 6.8 × 10^–12 mol/L, respectively, with 91% signal retention after five cycles, demonstrating robust anti-interference against ions (e.g., Cl^–, ${\rm SO}^{2-}_4 $) and organic impurities, attributed to the hydrophobic porous structure and stable Ru coordination. In conclusion, the Ru-COF composite represents a breakthrough in SERS substrate design by achieving ultrasensitive detection through EM-CM synergy, with key physical outcomes including high EF, sub-picomolar LODs, and exceptional spatiotemporal stability. This work provides a novel paradigm for metal-embedded COFs in plasmonic sensing and lays the groundwork for practical applications in environmental monitoring, food safety, and biomedical diagnostics.