CI-DL-MHCS represents designed central impact-inlet double layered microchannel heat sinks which shows the principal heat transfer feature, and the novel bifurcation is added on upper/lower deck in CI-DL-MHCS, namely CI-DL-MHCS-UB/LB, to explore the further overall thermal advantages numerically and experimentally. The internal located bifurcation parameters including position in CI-DL-MHCS and length have been investigated in the work with the coolant velocities in the range of 0.25–1.05 m/s. The calculated models in simulation is set as symmetric boundary condition, while the assumptions including RNG k-ε turbulence flow and incompressibility dominate in the paper. Bifurcation located lower deck of CI-DL-MHCS has been shown to be effective in controlling the substrate temperature, with a reduction in peak temperature of >18 K compared to referenced CI-DL-MHCS. Numerical simulations clearly demonstrate the enhancement of heat transfer caused by impingement jets and novel located bifurcations with experimental verification. Besides, CI-DL-MHCS with bifurcation have an average Nusselt number enhancement by 4.47% higher compared with CI-DL-MHCS without bifurcation. The bifurcation inevitably occupies the space in CI-DL-MHCS, resulting in a higher pressure drop penalty than the proposed bifurcated structure CI-DL-MHCS, but this can be balanced by an increase in heat transfer considering the overall thermal performance factor. Thus, CI-DL-MHCS featured with bifurcation located in CI-DL-MHCS-LB_3 outperforms significantly in overall thermal performance and thermal uniformity on substrate among all the designed tested models.