The lobe dynamics and mass transport between separation bubble and main flow in flow over airfoil are studied in detail, using Lagrangian coherent structures (LCSs), in order to understand the nature of evolution of the separation bubble. For this problem, the transient flow over NACA0012 airfoil with low Reynolds number is simulated numerically by characteristic based split (CBS) scheme, in combination with dual time stepping. Then, LCSs and lobe dynamics are introduced and developed to investigate the mass transport between separation bubble and main flow, from viewpoint of nonlinear dynamics. The results show that stable manifolds and unstable manifolds could be tangled with each other as time evolution, and the lobes are formed periodically to induce mass transport between main flow and separation bubble, with dynamic behaviors. Moreover, the evolution of the separation bubble depends essentially on the mass transport which is induced by lobes, ensuing energy and momentum transfers. As the results, it can be drawn that the dynamics of flow separation could be studied using LCSs and lobe dynamics, and could be controlled feasibly if an appropriate control is applied to the upstream boundary layer with high momentum.