In high bypass ratio engines, the flow exits the interturbine duct (ITD) and enters the low-pressure (LP) turbine. This paper aims to understand the effects of the boundary layer at the exit of ITD on the endwall secondary flows and loss of the first blade row in a low-pressure turbine. From the Navier–Stokes equations, the loss is decomposed into the parts generated by the mean vortex as well as turbulence theoretically. The result of computational fluid dynamics (CFD) shows that the incoming boundary layer from the ITD increases the total pressure loss coefficient by 14% compared to the case with uniform inlet condition. Although the distribution of the secondary vortices is strongly affected by the inlet boundary layer, the loss generated by the mean vortex within the blade passage is hardly affected. The analysis based on the turbulent dissipation shows that the dominant factor leading to the loss increase is the turbulent dissipation downstream of the blade trailing edge (TE) near the hub. The mixing process of the wake and the strong counter-rotating vortex pair (CVP) increases the turbulent dissipation significantly. It is also found that a simplified incoming boundary layer defined by the Prandtl's one-seventh power law can not reproduce the complex effects of the incoming boundary layer from the ITD.