Although corn germ meal is a rich source of dietary fiber, it contains a relatively low proportion of soluble dietary fiber (SDF) and is frequently contaminated with high levels of zearalenone (ZEN). Solid-state fermentation has the dual effects of modifying dietary fiber (DF) and degrading mycotoxins. This study optimized the solid-state fermentation process of corn germ meal using Bacillus subtilis K6 through response surface methodology (RSM) to enhance SDF yield while efficiently degrading ZEN. Results indicated that fermentation solid-to-liquid ratio and time had greater impacts on SDF yield and ZEN degradation rate than fermentation temperature. The optimal conditions were determined as temperature 36.5 °C, time 65 h, and solid-to-liquid ratio 1:0.82 (w/v). Under these conditions, the ZEN degradation rate reached 96.27 ± 0.53%, while the SDF yield increased from 9.47 ± 0.68% to 20.11 ± 1.87% (optimizing the SDF/DF ratio from 1:7 to 1:3). Scanning electron microscopy (SEM) and confocal laser scanning microscope (CLSM) revealed the structural transformation of dietary fiber from smooth to loose and porous forms. This structural modification resulted in a significant improvement in the physicochemical properties of dietary fiber, with water-holding capacity (WHC), oil-holding capacity (OHC), and water-swelling capacity (WSC) increasing by 34.8%, 16.4%, and 15.2%, respectively. Additionally, the protein and total phenolic contents increased by 23.0% and 82.61%, respectively. This research has achieved efficient detoxification and dietary fiber modification of corn germ meal, significantly enhancing the resource utilization rate of corn by-products and providing technical and theoretical support for industrial production applications.