Direct numerical simulations are conducted to investigate the transition flow over a flat plate featuring pressure gradients and a three-dimensional rough surface. The rough surface is categorised into nine types based on the effective slope ratio ${E{{S}_{z}}}/{E{{S}_{x}}}$ ($ES_{z}$: spanwise effective slope, $ES_{x}$: streamwise effective slope) and skewness $Sk$, with the embedded boundary method employed for resolving the solid wall. Findings indicate that the influence of ${E{{S}_{z}}}/{E{{S}_{x}}}$ on the streamwise vortex pair counters the effects on the wall-normal shear and the two-dimensional spanwise vortex sheet. Negative skewness alone can stimulate all three components of the hairpin vortex simultaneously. The new formula for predicting the sheltering angle, which incorporates the up-ejecting segment, demonstrates enhanced accuracy in predicting the sheltering area across the entire rough surface, outperforming the previous formulation. The forward displacement relative to the drag peak of the pressure stagnation point along the streamwise direction remains unaffected by the spanwise effective slope and the skewness. In the upper transition region, negative skewness significantly intensifies both the production and dissipation terms of the fluctuating kinetic energy, which correlate with the inviscid instability of the separation flow and the viscous instability induced by the lift-up mechanism. During the early phase of transition, negative skewness is capable of producing linear modes that match the intensity of nonlinear coherent structures at intermediate to high frequencies, exhibiting quasi-orthogonality. During the late transition phase, zero skewness can give rise to linear modes featuring robust quasi-orthogonality at low frequencies.