To improve the performance of a clay liner in blocking the volatile organic contaminants(VOCs)at the bottom of a landfill, a mathematical model intended to study the migration of VOCs through the clay liner with bubbles was established based on the convection-diffusion-adsorption mechanism. Other mechanisms, including consolidation deformation of the clay liner with disconnected bubbles, intrinsic biodegradation of VOCs, and transferring of VOCs between the liquid and solid phases, were integrated in the newly proposed model. Using an actual project as an example, the mathematical model was solved with a finite element software for multiple physical fields, and the transfer and transformation of representative VOCs through the clay liner were investigated. The results show that the retardation effect of vapor formed by the trapped bubbles can impede the break of typical VOCs through the clay liner to some extent. In particular, when the gas in the bubbles is oxygen, significant intrinsic biodegradation of VOCs due to the presence of oxygen can efficiently block the VOCs, and the bubble wall layer is relatively thin under common concentration conditions of pollutants in landfills.