Surface-enhanced Raman scattering (SERS) features a unique fingerprint spectrum for fast and highly sensitive non-destructive detection without sample pretreatment. Aiming at the problem of few "hot spot" and uneven distribution of traditional SERS substrate, in this work, a surface-enhanced Raman substrate of silica/carbon nanotubes/silver nanoparticles (SiO2/CNTs/AgNPs) with high on all sides and low in the middle was synthesized by hydrothermal synthesis. The AgNPs were characterized by transmission electron microscopy (TEM), and the average diameter was 38 nm to 63 nm. The substrate exhibited high sensitivity, stability, and uniformity with a detection limit of 10−12 M for rhodamine 6G (R6G). Furthermore, we conducted an in-depth research on the enhancement contribution of the substrate by finite-difference time-domain (FDTD); the simulation results were in good agreement with the experimental results. Finally, the substrate was used for the detection of phenol red in water; the results showed that the Raman intensity was exponentially related to the concentration of phenol red solution with the coefficient of determination R2 = 0.99991, which provided a new method for detecting water pollutants. [ABSTRACT FROM AUTHOR]