Bacillus amyloliquefaciens fmbJ belongs to Gram-positive bacteria, which can secrete a series of antimicrobial substances, including lipopeptides. Among them, bacillomycin D (BD) has strong antifungal activity for wide range of applications. However, the current yield of BD cannot meet the requirements of industrial production. In this study, Plackett-Burman and Box-Behnken were used to optimize diatomaceous earth (DE) immobilized fmbJ for BD production. And the optimal conditions were obtained as 50 mL of fermentation medium (250-mL shake flask) with an inoculum of 6.38 %, fermentation at 33 °C 180 rpm for 72 h, and addition of 0.31 g DE at 15.48 h. The model predicted a yield of 947.01 mg/L and obtained 942.33 ± 5.46 mg/L after validation. The optimal condition was used for cyclic fermentation, and the results of three fermentations were 1101.31 mg/L, 1047.83 mg/L and 662.72 mg/L, which were higher than the free fmbJ. The results of fermentation parameters, intracellular amino acids and genes expression showed that immobilized fmbJ could accumulate amino acids related to BD synthesis, especially Glu, faster still have better stability, longevity and use time at rapid fermentation. Therefore, the index parameters of this study could provide a reference for the subsequent industrial production of BD.