A detailed understanding of the catalytic upgrading of light cycle oil (LCO) is important to achieve effective deep hydrodesulfurization (HDS) when LCO is mixed with straight run gas oil in the diesel pool. Herein, HDS of polyaromatic-rich LCO was studied at the molecular level over three NiMo catalysts on silica–alumina supports, which were synthesized on the pilot scale using different silica/alumina mixing procedures. Gas chromatography with atomic emission detection and two-dimensional gas chromatography with time-of-flight mass spectrometry were used to evaluate the HDS performance through determining the feed and product compositions, respectively, at the molecular level. Furthermore, the textural properties of the catalysts were evaluated using Raman spectroscopy, transmission electron microscopy, and the temperature-programmed desorption of NH3. The performance of the best catalyst was attributed to its higher content of octahedrally coordinated Mo oxide species, a lower number of layered stacks, and the more acidic sites on the surface. In addition, the hydrotreating reactivity of various family groups in LCO over the catalyst was investigated.