Boundary layer transition induced by surface roughness elements plays an important role in aerodynamic and aero-thermodynamic design of subsonic/supersonic/hypersonic vehicles. However, the effect of three-dimensional isolated roughness element in the process of promoting/suppressing boundary layer transition is far from being fully understood, particularly in the incompressible laminar flow. In the present study, the laminar-to-turbulent transition induced by a three-dimensional isolated micro-ramp element immersed in an incompressible laminar boundary layer is investigated numerically. The embedded large eddy simulation (ELES) combining the intermittency transition model and the wall-modeled large eddy simulation (WMLES) S − Ω model is employed for the first time. Numerical results on the time-averaged/instantaneous flow field and the statistical flow fluctuations are analysed and validated thoroughly by the existing experimental measurements. It is found that the interaction of the secondary and the tertiary streamwise vortices causes a high level of wall shear and an inflectional velocity distribution in the near-wall region. An additional eddy system that develops nonlinearly from the unstable inflectional flow may trigger the boundary layer transition. The present study validates that the ELES combined with the WMLES S − Ω model is an efficient simulation tool for industrial wall-bounded flows allowing effective compromise between flexibility, cost, and accuracy.