A novel bis(indolyl)methane-modified silica reinforced with multiwalled carbon nanotubes sorbent for solid-phase extraction was designed and synthesized by chemical immobilization of nitro-substituted 3,3′-bis(indolyl)methane on silica modified with multiwalled carbon nanotubes. Coupled with high-performance liquid chromatography analysis, the extraction properties of the sorbent were evaluated for flavonoids and aromatic organic acid compounds. Under optimum conditions, the sorbent can simultaneously extract five flavonoids and two aromatic organic acid preservatives in aqueous solutions in a single-step solid-phase extraction procedure. Wide linear ranges were obtained with correlation coefficients (R²) ranging from 0.9843 to 0.9976, and the limits of detection were in the range of 0.5–5 μg/L for the compounds tested. Compared with the silica modified with multiwalled carbon nanotubes sorbent and the nitro-substituted 3,3′-bis(indolyl)methane-modified silica sorbent, the developed sorbent exhibited higher extraction efficiency toward the selected analytes. The synergistic effect of nitro-substituted 3,3′-bis(indolyl)methane and multiwalled carbon nanotubes not only improved the surface-to-volume ratio but also enhanced multiple intermolecular interactions, such as hydrogen bonds, π–π, and hydrophobic interactions, between the new sorbent and the selected analytes. The as-established solid-phase extraction with high-performance liquid chromatography and diode array detection method was successfully applied to the simultaneous determination of flavonoids and aromatic organic acid preservatives in grape juices with recoveries ranging from 83.9 to 112% for all the selected analytes.