The safety of transgenic food has been paid the most attention to by the public and scientists. Trace metal bioavailability could provide information for safety assessment of transgenic food. The critical functional digestion and absorption in the gastrointestinal tract were simulated by bionic gastrointestinal digestion, metabolism of gut microbiota, and bionic biomembrane adsorption with liposome and then used for the pretreatment of transgenic and general soybeans. Ni speciation in the chyme was defined as affinity-liposome and water soluble Ni. Nickel bioavailability was assessed by the content of affinity-liposome Ni. .Water soluble Ni was the main species of nickel complex in the chyme. Nickel bioavailability was 4.1% for transgenic soybean and 3.3% for general soybean, which could be enhanced by gastrointestinal digestion and metabolism of gut microbiota. After transgene, nickel bioavailability was increased 24% but the content of affinity-liposome Ni was 122.3 ng·g-1 for transgenic soybean, just as 36% as that of general soybean.