A series of MOF-derived ZrO2-supported Pd-Ni bimetallic catalysts (PdNi/UiO-67-CTAB(n)-A500) were prepared by co-impregnation and pyrolysis at 500 °C under air atmosphere using UiO-67-CTAB(n) (CTAB: cetyltrimethylammonium bromide; n: the concentration of CTAB; n = 0, 3, 8, 13, 18) as a sacrificial template. The catalytic activity of PdNi/UiO-66-CTAB(n)-A500 in 1,3-butadiene hydrogenation was found to be dependent on the crystal morphology of the UiO-67 template. The highest activity was observed over the PdNi/UiO-67-CTAB(3)-A500 catalyst which was synthesized using UiO-67-CTAB(3) with uniform octahedral morphology as the template for the 1,3-butadiene selective hydrogenation. The 1,3-butadiene conversion and total butene selectivity were 98.4% and 44.8% at 40 °C within 1 h for the PdNi/UiO-67-CTAB(3)-A500 catalyst, respectively. The catalyst of PdNi/UiO-67-CTAB(3)-A500 can be regenerated in flowing N2 at 200 °C. Carbon deposited on the surface of the catalyst was the main reason for its deactivation. This work is valuable for the high-efficiency bimetallic catalyst’s development on the selective hydrogenation of 1,3-butadiene.