Product inhibition is the main problem of high-strength rice vinegar fermentation by Acetobacter pasteurianus. An optimized semi-continuous operation mode was proposed with a modified starting-up protocol which can improve the average acetification rate 35 % higher than original one. First, we revealed PQQ-ALDH is the rate-limiting enzyme responsible for ethanol oxidation route, whose apparent K m of PQQ-ADH and PQQ-ALDH is 1.89 and 7.80 mM, respectively. Further work elucidated that PQQ-ALDH follows ordered Bi–Bi mechanism which indicated that Co Q can improve the reaction. Among five Co Q precursors, supplementation of 20 mM isopentenyl alcohol got the best result, which improved strain acid resistance ability that accelerates biomass accumulation. A two-stage starting-up protocol was developed, which reduced the duration of the starting-up process from 45 to 34 h. An optimized semi-continuous operation mode was proposed whose whole operation time reduced from 116 to 98 h and average acetification rate has been raised to 1.77 g/Lh, while the original is 1.31 g/Lh. The average activity of ALDH is 43 % higher than original process, while ADH is 19 %, which shows a good correlation with acetification rate.