Laminar-turbulent transition can affect the aerodynamic performance of low Reynolds number flyers, such as micro air vehicles that operate at the Reynolds number of 10 4-10 5. To gain better understanding of the fluid physics and the associated aerodynamics characteristics, we coupled a Navier-Stokes solver, the e N transition model, and a Reynolds-averaged two-equation closure to study the low Reynolds number flow characterized with the laminar separation bubble and transition. A new intermittency function suitable for low Reynolds number transitional flow incurred by laminar separation is proposed and tested. With the method, we investigate the performance of a rigid airfoil and a flexible airfoil, mounted with a flexible membrane structure on the upper surface, using SD7003 as the configuration. Good agreement is obtained between the prediction and experimental measurements regarding the transition location, aerodynamic coefficients, and overall flow structures. We also examine the impact of gust on the transition process and airfoil performance. We further investigate the effect of the flexible surface on the transition. We find that the self-excited flexible surface vibration affects the separation and transition positions; however, the time-averaged lift and drag coefficients are close to those of the rigid airfoil. Nomenclature = kinematic eddy viscosity = nondimensionalized time, tc=U ! = specific dissipation rate ! g = gust frequency