Hydrotreating of vacuum residue by ebullated-bed shows tremendous significance due to more stringent environmental regulations and growing demand for lighter fuels. However, enhancing the catalyst stability still remains as a challenging task. Herein, two Ni–Mo/Al2O3 catalysts with distinct morphologies (i.e., spherical and cylindrical) were first designed, and the morphology effect on deactivation was systematically elucidated employing multi-characterizations, such as HRTEM with EDX mapping, electron microprobe analysis, FT-IR, TGA and Raman. It is found that spherical catalyst exhibits superior hydrotreating stability over 1600 h. The carbonaceous deposits on spherical catalyst with less graphite structure are lighter, and the coke weight is also smaller. In addition, the metal deposits uniformly distribute in the spherical catalyst, which is better than the concentrated distribution near the pore mouth for the cylindrical catalyst. Furthermore, the intrinsic reason for the differences was analyzed by the bed expansion experiment. Higher bed expansion rate together with the better mass transfer ability leads to the enhanced performance. This work sheds new light on the design of more efficient industrial hydrotreating catalyst based on morphology effect.