Precedent mass transfer experiments and the corresponding large-eddy simulation (LES) by Oda et al. (Proc. 14th Intl. Heat Transfer Conf., IHTC14-23191, Washington, D.C., USA, Aug. 8-13, 2010) and Takeishi et al. (ASME Paper GT2012-69625, 2012) revealed that an inclined pin-fin channel with a wavy endwall shows better "endwall" heat transfer than that with a flat endwall with less or comparable pressure loss, as long as the pin-fin surface was treated as thermally adiabatic. Therefore, in this study, a conjugate heat transfer problem in the pin-fin channels was solved numerically to evaluate the overall heat transfer performance including heat transfer from the pin-fin surface. To this end, an LES-based conjugate heat transfer analysis was newly proposed, which utilizes time-mean velocity and turbulent statistics obtained by preliminary LES to estimate the eddy thermal diffusivity for thermal Reynolds-averaged NavierStokes (RANS) analysis to solve the conjugate heat transfer problem. This method has an advantage over conventional RANS-based methods when the time-mean flow field is difficult to predict due to the complex turbulent flows, e.g., massively separated flows in pin-fin channels. By applying the method to the inclined pin-fin channel with a flat or wavy endwall, it is clarified that the wavy endwall shows a clearly better overall heat transfer rate than the flat endwall when the Biot number is of the order of 10(-1), which represents a typical condition to cool combustor liners of jet engines.