The improved heat dissipation observed in 3D micro-ribbed tubes is primarily influenced by the intricate interplay of multiple structural parameters. Nevertheless, research into the coupling mechanisms of these multi-structural parameters remains constrained by the absence of effective methodology in numerical solutions. In the present work, a new 3D micro-rib structure based on discrete adjoint method is established. Firstly, the research examines the interplay of different parameters (such as arrangement, relative roughness height, angle of attack, and circumferential rows) on the thermo-hydraulic performance. It is noted that the heat transfer efficiency is notably impacted by the relative roughness height. And the arrangement methodology dictates the optimal positioning for heat transfer efficiency. An increase in the number of circumferential rows enhances fluid mixing, while the angle of attack plays a crucial role in the formation of longitudinal vortices. Secondly, the coupling optimization technique is employed to obtain the optimal structure featuring non-uniform relative roughness height by the developed numerical solution. Overall, in comparison to the smooth tube, the optimized ribbed tube exhibits a remarkable 64.9% enhancement in performance evaluation criteria. Finally, a notable enhancement of 10.65–22.78% is observed when comparing with the prevailing micro-rib structures.