A method for monitoring the concentration changes of organic acids in the fermentation process of Clostridium acetobutylicum by capillary ion electrophoresis has been developed. In this study, 4-methoxybenzoic acid was used as the background electrolyte for the indirect ultraviolet detection, and cetyltrimethylammonium chloride (CTAC) was employed as the electroosmotic flow modifier. The sample of fermentation was simply treated by centrifugation and dilution. The optimal conditions for the separation were established as 10 mmol/L of 4-methoxybenzoic acid solution (pH 5. 8) and 0. 15 mmol/L of CTAC solution. The limits of quantification for lactate, acetate and n-butyrate were 1.22, 0.38 and 0.58 mg/L, respectively. The method can be successfully used for the metabolic flux analysis of Clostridium acetobutylicum.