Abstract: The design procedure of transonic natural laminar wings can benefit significantly from efficient transition prediction software capable of handling complex aerodynamic geometries. In this article, Commercial Aircraft Corporation of China Ltd (COMAC) Beijing Aircraft Technology Research Institute developed a Computational Fluid Dynamics software CFAST to obtain laminar base flows. CFAST is highly efficient; it only costs 200 seconds per case. The output of CFAST is then integrated into a transition prediction module to perform fast transition prediction of three-dimensional transonic back-swept wing boundary layers. The transition prediction module adopts the dual-e^N criterion from the linear stability theory so that both Tollmien-Schlichting and stationary crossflow modes can be considered. Since open-source experimental data of high-Reynolds-number laminar flows are rare, the standard research model CRM-NLF designed by NASA is utilized to study the effects of the attack angle, Reynolds number, and Mach number on the transition prediction. The transition prediction results agree well with those obtained by RANS with transition models, suggesting that the method is of great potential in designing and optimizing of transonic natural laminar wings.