Flutter seriously affects the safety and reliability of aeroengine. The blade mistuning is inevitable due to machining error and service wear, which has a significant influence on flutter stability. In this paper, the eigenvalue method is used to calculate the aerodynamic damping of transonic fan blades of civil aviation engine at different nodal diameters (NDs) and structural modes. The results show that under the design condition, the first three structural modes of the blade are aero-elastic stable for each ND, and the aerodynamic damping gets the minimum at ND1 for the first bending mode. As the back pressure deviates from design condition towards stall, the aerodynamic damping obviously decrease and even negative aerodynamic damping occurs at normalized mass flow rate of 0.930. Six kinds of mistuning patterns are considered based on the eigenvalue method, divided into two categories: structural mistuning and aerodynamic mistuning, where structural mistuning includes alternate mistuning, sinusoidal mistuning and random mistuning. The alternate mistuning has better improvement on flutter suppression than the sinusoidal mistuning with the same frequency offset, though further increasing the amount of mistuning cannot provide extra aero-damping when the frequency offset reaches a critical value of 7%. For the aerodynamic mistuning, the improvement of aero-damping is limited in comparison with the structural mistuning, especially for the random mistuning through Monte Carlo simulations. Based on the analysis of eigenvectors, the single blade aerodynamic mistuning breaks the periodic pattern in travelling wave mode, which tends to make the aero-elastic systems stable. While the symmetry group mistuning maintains the periodicity and destabilizes the aero-elastic system.