Douchi is popular in China as a fermented soybean food. The effects of NaCl on the isoflavone contents and composition during processing of douchi, as well as the β-glucosidase activity was investigated. The results indicate that 61% of the isoflavones in raw soybeans were lost when NaCl content was 10%, which is mainly attributed to pre-fermentation (43%) and post-fermentation (18%) during douchi processing. While a pre-treatment did not generate major differences in total isoflavone content during douchi processing, isoflavone composition was altered. The levels of aglycones increased, while the corresponding levels of β-glucosides, malonylglucoside and acetylglucoside decreased. Further, isoflavones in the form of aglycones exceeded 90% of total content following post-fermentation. Finally, changes in isoflavone isomer distribution were found to be related to β-glucosidase activity during fermentation, which was affected by NaCl supplementation.