The work aims to study the migration law of residual toluene from baking paper to food and investigate the effect of baking paper microstructure on the migration. In this research, the GC-MS/MS method was used to analyze the migration law of residual toluene from baking paper into food simulants (olive oil, Tenax-TA) under different conditions of baking temperature, time, paper quantification, initial toluene content, microwave heating, etc., and the microstructure changes of baking paper before and after migration. The results showed that, the migration rate varied markedly with the temperature, with higher temperatures leading to accelerated migration. The longer the migration, the greater the migration rate. However, after the migration lasted for more than 40 min, the migration rate of toluene into Tenax-TA shifted to a downward trend significantly. The higher the gram weight of paper, the lower the toluene migration rate. The initial concentration of toluene in baking paper had no significant effect on the migration rate. The higher the microwave power, the higher the migration rate. As the microwave time lengthened, the migration rate rose first and then dropped. The scanning electron microscope (SEM) results suggested that baking at a high temperature could change the internal fiber structure of paper, and lead to an increasing size and number of fiber holes. Residual toluene in baking paper migrates to food simulants under certain conditions. This makes it easier for toluene molecules to pass through the pores into the food, thus accelerating migration.