Abstract: In the design of the nacelle outer cover profile, it is crucial to maintain the boundary layer's laminar state to minimize wall friction and enhance payload capacity. Understanding the boundary-layer transition mechanisms and accurately predicting the transition front is fundamental to effectively evaluate different designs of the nacelle. In this work, we focus on the stability characteristics of boundary layers over nacelle with three different outer covers under cruise conditions. Considering transition mechanisms correlated with the T-S waves and the shock wave-induced separation bubbles, the transition fronts are predicted. The results indicate that as the unfavorable pressure gradient increases, T-S waves become more unstable, leading to earlier boundary-layer separation. Therefore, maintaining a relatively large range of favourable pressure gradient as well as reducing unfavorable pressure gradient will delay the boundary-layer transition. In addition, for a scaled nacelle model, the predicted transition front and that obtained in wind tunnel tests are morphologically similar, confirming the validity of the prediction method.