Electrooxidation of organics using electrons as oxidants is a clean approach to produce commodity chemicals. However, designing an electrocatalyst with superior performance at low cell voltage remains a challenge. In this study, a series of VS-Co@Co9S8 electrocatalysts were fabricated by thermal reduction method using MOFs as templates. The catalytic oxidation performance and reaction mechanism of such specimens for benzyl alcohol were comprehensively analyzed by electrochemical measurement method and ex-situ structure characterization. The results show that Co@Co9S8-30 M has a unique three-dimensional (3D) micro cubic structure with abundant S vacancy (VS). These features accelerate the electrons and substrate transfer as well as provide plentiful active sites for benzyl alcohol electrooxidation reaction (BAOR). Consequently, the Co@Co9S8-30 M presented outstanding catalytic activity. The overpotential of 10 mA cm−2 (η10) was only 265.4 mV for BAOR. The conversion rate and benzoic acid selectivity were achieved to 72% and 90%, respectively. Particularly, the formation rate of benzoic acid was 7.247 mmol·gcat.−1·h−1. Moreover, the Co@Co9S8-30 M exhibited superior durability over 135 h. The coordination number of octahedral metal sites in Co9S8 did not match the number of Co 3 d orbital electrons, resulting in the weakening of bonding strength between Co and S elements. Thus, the Co@Co9S8 was reconstructed to Co3O4@CoOOH. Based on this assessment, the Co3O4@CoOOH was the active site of BAOR. This work provides theoretical guidance for the design of Co-based catalysts.