Micro-channel heat sink (MCHS) has been extensively used in various electronic cooling fields. Double-layered MCHS, or DL-MCHS, is regarded as one effective technique for high-heat-flux transfer and is expected to meet the ever-increasing heat load requirement of future electronic device generations. In order to improve the cooling capacity, two new types of the MCHS, with a double-layered matrix structure (DL-M) and double-layered interlinked matrix structure (DL-IM) are proposed and investigated numerically. The two designs are compared with the traditional double-layered rectangular structure (DL-R) and the double-layered triangular structure (DL-T). Different properties of the heat sink are investigated to assess the overall heat transfer performance, for which coolant flow and heat transfer are both evaluated. The numerical results reveal that the periodical slot subchannel in the matrix has a significant effect on fluid flow for heat transfer. In comparison to the DL-R and the DL-T, the DL-M and DL-IM realize a much lower pressure drop and temperature rise at the base surface and also have higher Nusselt number and secondary flow intensity, therefore, manifesting better overall thermal performance. In the DL-M and DL-IM, the coolant flows along the periodical subchannel in one layer and is redirected into the second layer with vortices being induced. The vortices promote the coolant mixing and enhance the mass and heat transfer. These geometric design strategies can provide references for wide heat sink applications.