This work reports the morphological investigation of nanostructured sulfided CoMo catalysts by means of high-resolution transmission electron microscopy (HRTEM). The catalysts were supported on Ti-modified hexagonal mesoporous silica (HMS-Ti) and P-modified HMS-Ti (P/HMS-Ti) materials. The oxide precursors were characterized by specific surface area (SBET), temperature-programmed reduction (TPR), diffuse reflectance infrared Fourier transform spectroscopy in the OH region (DRIFTS-OH) and X-ray photoelectron spectroscopy (XPS) in order to elucidate the influence of the impregnation sequence (successive vs. simultaneous) and the effect of P-incorporation into HMS-Ti material on the morphology of calcined CoMo catalysts. Both TPR and XPS measurements indicate that the catalysts prepared by successive impregnation possess well-dispersed MoO3 and CoO phases, whereas their counterparts prepared by simultaneous impregnation additionally possess the CoMoO4 phase. For all sulfided catalysts, the presence of MoS2 phase with particle size in the range 3.3–4.4 nm was confirmed by HRTEM. Catalytic activity was evaluated in the reaction of hydrodesulfurization (HDS) of dibenzothiophene (DBT) carried out in a flow reactor at 593 K and hydrogen pressure of 5.5 MPa. P-incorporation into the HMS-Ti material led to an overall increase in HDS activity and the hydrogenation ability of the sulfided catalysts. All catalysts proved to be stable during 10 h time-on-stream (TOS) operation. The activity of sulfide catalysts in the target reaction depends linearly on the surface exposure of Co species in the oxide precursors, as determined by XPS, and on the morphology of the sulfide form of catalysts (surface density of MoS2 particles and their sizes) as determined by HRTEM.