The biological detoxification of lignocellulose hydrolysate is an effective method through which to enhance microbial fermentation efficiency. In this study, an inhibitor-tolerant strain of A. niger (Aspergillus niger) was used for the biological detoxification of corncob hydrolysate. The results showed that A. niger M13 can tolerate a concentration of at least 7.50 ± 0.19 g/L of acetic acid, 1.81 ± 0.13 g/L of furfural, and 1.02 ± 0.10 g/L of HMF (5-Hydroxymethylfurfural). The spores had a higher detoxification efficiency than the mycelial pellets with a detoxification rate of 0.1566 g/L/h, 0.1125 g/L/h, and 0.015 g/L/h for acetic acid, furfural, and HMF, respectively. The cell preferentially consumed furfural, then HMF, before simultaneously degrading acetic acid and glucose. A. niger M13 spores could accumulate small amounts of citric acid directly from undetoxified hydrolysate at a concentration of about 6 g/L. Therefore, A. niger M13 can serve as an excellent biological detoxification strain and a potential citric acid fermenting strain when using undetoxified lignocellulosic hydrolysates.