Detailed experimental investigation was carried out to investigate the interaction of unsteady wakes with boundary layer in a high-lift low-pressure turbine. Extensive measurements about boundary layer character were conducted using hot-film and hot-wire methods. In-depth analysis of the effect of wake passing frequency on boundary layer transition was carried out. The strength of separation control and profile loss variation at two wake passing frequencies were also studied. The results show that wake-induced transition can be detected in the separating shear layer, and complex vortex structures are induced by the interaction between the negative jet of wake and separation bubble. The proportions of laminar, separation and turbulence friction loss in the total loss vary with wake passing frequency, which leads to the change in the total boundary layer loss. In particular, as the wake passing frequency changes, the laminar and turbulent friction loss show opposite trends, and this indicates that the best frequency can be achieved by balancing these two types of losses. For a given high-lift profile, an optimum wake passing frequency that will lead to the minimum loss exists.