The toxicity of ginkgo kernel is a global concern, restricting its consumption as a medicinal food. This study focuses on eliminating the toxic components, specifically ginkgolic acid, from ginkgo kernel juice. The approach used was probiotic fermentation with autochthonous lactic acid bacteria combined with macroporous resin. Compared to using lactic acid fermentation alone, adding macroporous resin during probiotic fermentation significantly enhanced the removal of toxic ginkgolic acid and 4'-O-methylpyridoxine from ginkgo kernel juice. After 48 h of fermentation with macroporous resin, the contents of ginkgolic acid and 4'-O-methylpyridoxine decreased by more than 69% and 61%, respectively. Interestingly, the adsorption of microbial growth inhibitors, such as ginkgolic acid, 4'-O-methylpyridoxine, and phenolics, by the resin did not hinder the growth of lactic acid bacteria or their metabolic activities involving organic acids and monosaccharides. The study further confirmed that microbial adsorption was the primary reason for removing ginkgolic acid during probiotic fermentation. Also, the adsorption mechanism of ginkgolic acid during probiotic fermentation with macroporous resin was explored. From a mass transfer perspective, incorporating macroporous resin during the probiotic fermentation of ginkgo kernel juice reduced the mass transfer resistance for surface diffusion. Consequently, this lowered the contribution of surface diffusion to the overall diffusion process and facilitated the efficient removal of toxic ginkgolic acid. This work can help to understand the physical mechanism regarding detoxification of ginkgo kernel juice by probiotic fermentation, and offer potential strategies to enhance the safety of ginkgo kernel products.