This study was conducted to compare the potential ameliorative effects between probiotic Bacillus subtilis and biodegradable Bacillus subtilis on zearalenone (ZEN) toxicosis in gilts. Thirty-six Landrace×Yorkshire gilts (average BW = 64 kg) were randomly divided into four groups: (1) Normal control diet group (NC) fed the basal diet containing few ZEN (17.5 μg/kg); (2) ZEN contaminated group (ZC) fed the contaminated diet containing an exceeded limit dose of ZEN (about 300 μg/kg); (3) Probiotic agent group (PB) fed the ZC diet with added 5 × 109 CFU/kg of probiotic Bacillus subtilis ANSB010; (4) Biodegradable agent group (DA) fed the ZC diet with added 5 × 109 CFU/kg of biodegradable Bacillus subtilis ANSB01G. Results showed that Bacillus subtilis ANSB010 and ANSB01G isolated from broiler intestinal chyme had similar inhibitory activities against common pathogenic bacteria. In addition, the feed conversion ratio and the vulva size in DA group were significantly lower than ZC group (p < 0.05). The levels of IgG, IgM, IL-2 and TNFα in the ZC group were significantly higher than PB and DA groups (p < 0.05). The levels of estradiol and prolactin in the ZC group was significantly higher than those of the NC and DA groups (p < 0.05). Additionally, the residual ZEN in the feces of the ZC and PB groups were higher than those of the NC and DA groups (p < 0.05). In summary, the ZEN-contaminated diet had a damaging impact on growth performance, plasma immune function and hormone secretion of gilts. Although probiotic and biodegradable Bacillus subtilis have similar antimicrobial capacities, only biodegradable Bacillus subtilis could eliminate these negative effects through its biodegradable property to ZEN.