Bacillus subtilis ANSB060 from the fish gut had strong ability to detoxify aflatoxins. The aim of this research was to investigate the protective effect of B. subtilis ANSB060 (ANSB060) on egg quality and biochemical and histopathological changes of liver and kidney in laying hens when exposed to aflatoxin B(1). Treatments (C20, C40, and C60) were prepared by substituting corn contaminated by aflatoxin B(1) (AFB1) at different proportions (20, 40, and 60%) for normal corn in basic diets. The aflatoxin degradation enzyme (E) treatments (E20, E40, and E60) were mixed with the fermentation liquor of ANSB060 with C20, C40, and C60, respectively. The results showed that ANSB060 can improve the eggshell strength in E60 compared with C60 (P ≤ 0.05), and toxin reduced the content of total protein (in groups C20, C40, and C60) and albumin (in C20 and C40; P < 0.05) and heightened the activities of GPT (in C60) and GOT (in C40 and C60) in serum (P < 0.05). In the liver, AFB1 inhibited the activity of superoxide dismutase and glutathione peroxidase (C40 and C60; P < 0.05) and increased the content of malonaldehyde (in C40 and C60), which induced the damage in the liver and kidney as shown in the photomicrographs of hematoxylin and eosin-stained sections. The addition of ANSB060 can enhance the activity of antioxidant enzymes, and it recovered the protein synthesis in liver. Moreover, ANSB060 also ameliorated the damage of liver and kidney tissue and restored them to normal. Hence, ANSB060 had the ability to inhibit the damage induced by AFB1; it will have a great potential in industrial applications.