Two experiments were conducted to optimize the fermentation of cottonseed meal by Cellulosimicrobium funkei (C. funkei) for the ability of the bacteria to degrade aflatoxin B1 (AFB1) and then to evaluate the bacterial detoxification in ducklings. In experiment 1, the fermentation of cottonseed meal by C. funkei was improved by changing the inoculation amounts by 10% (108 cfu/mL), using a 1:0.5 material to water ratio at 35°C temperature for a 144 h reaction duration, which resulted in an 83.4% biodegradation of AFB1. In experiment 2, 112 one-day-old male Cherry Valley ducklings were randomly allocated to 4 experimental groups with 4 replicates of 7 birds each. For a period of 2 wk the controls received a base duckling diet (BD), a second group received a base diet contaminated with 10% AFB1 cottonseed meal (96.8 μg AFB1/kg), a third group was fed a base diet added with 5% unfermented and 5% fermented AFB1-contaminated cottonseed meal (57.0 μg AFB1/kg), and the fourth group was fed a base diet added with 10% AFB1-contaminated fermented cottonseed meal (16.0 μg AFB1/kg). The growth performance, relative organ weights, and serum biochemistry were analyzed. The results showed that the feed conversion ratio in the second group was lower than that of the controls at wk one and 2 (P < 0.05). Also, after 2 wk, group 2 ducklings had increased relative weights of the liver, kidneys, and spleen, increased activities of alanine aminotransferase (ALT) and aspartate aminotransferase (AST), increased concentration of blood urea nitrogen (BUN) and creatinine (Crt), and decreased relative weight of Fabricius bursa (P < 0.05). In addition, the concentrations of total protein (TP) and albumin (ALB) in serum were also significantly higher at weeks one and 2 (P < 0.05). These alterations were attenuated or prevented when 5 or 10% fermented cottonseed meal substituted equal amounts of unfermented cottonseed meal in the diet. In conclusion, fermentation of AFB1-contaminated feed materials by C. funkei offers a new strategy to reduce the negative effects of aflatoxicosis in ducklings.