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In this study, black soybean was firstly processed by solid-state fermentation (SSF) with a probiotic fungus Eurotium cristatum YL-1. The effect of SSF on the nutritional components (including proximate, amino acids, minerals, and fatty acids), total phenolics, isoflavones, antioxidant activity, and volatile organic compounds of black soybeans were revealed. Results of this work demonstrated that black soybean processed by SSF with E. cristatum greatly increased the contents of protein, essential amino acids, and some minerals (e.g., calcium, phosphorus, and magnesium). GC results revealed that more than 80% of the total lipids from both fermented and non-fermented black soybeans were unsaturated fatty acids, and SSF influenced the fatty acids composition. Higher contents of total phenolics and aglycone isoflavones (i.e., genistein, daidzein, and glycitein) of fermented black soybeans were achieved by SSF. Furthermore, SSF with E. cristatum considerably augmented the ferric reducing antioxidant power, scavenging effects against ABTS·+ and DPPH radical, reducing power, and chelating ability of black soybeans, which evaluated with various polarity solvent extracts. HS-GC-IMS analysis detected a total of 66 volatile compounds in FBS and BS, and 56 volatile organic compounds were successfully identified. The intensities of main volatile compounds (i.e., 10 esters, 11 alcohols, and 19 aldehydes) differed remarkably by fermentation with E. cristatum. The intensities of seven alcohols and nine aldehydes considerably decreased, whereas higher levels of esters were achieved by SFF. Thus, our results confirmed that black soybeans processed by SSF with E. cristatum is a promising approach to substantially improve its nutritional value, flavor characteristics, and biological effect, and might have great potential in the development of new functional foods or be used as a new nutritional ingredient applied in food design.