•Co(Ni)Mo catalysts were synthesized from heteropoly compounds and C-coated Al2O3.•Catalytic activity was essentially dependent on carbon content in carrier.•Carbon content influences the morphology of active phase and catalytic properties.•Concept of interlayer dynamics is helpful in establishing structure–activity relations for TMS. Effects of activated carbon of a carbon-coated alumina support and active phase morphology of transition metal sulfide (TMS) catalysts in hydrotreatment (HDT) of S-containing compounds were studied. The catalysts were synthesized from Anderson-type heteropoly compounds and characterized with multiple methods: X-ray powder diffraction, N2 physisorption, temperature-programmed desorption of ammonia, pyridine-adsorbed Fourier transform infrared spectroscopy, H2 temperature-programmed reduction, and high-resolution transmission electron microscopy. The catalysts were tested in hydrodesulfurization (HDS) of thiophene, dibenzothiophene and HDT of diesel. The results suggest that the catalytic activity in HDS and hydrogenation reactions depends on the shape of crystallites of the active phase. The results are interpreted using recently proposed concept of interlayer dynamics. This concept is helpful in establishing structure–activity relations for TMS.