Among the advanced integrated circuit (IC) integration methods, three-dimensional heterogeneous integration with through-silicon via (TSV) technology showed great potential towards the system-level integration with an increased interconnect density in a smaller footprint. However, the heat mitigation across several dies remains a critical issue in this technology with the utilization of vertical dimension, and the distributed hotspots in 3D ICs generating heat-fluxes up-to hundreds of W cm-2 to few thousands of W cm-2. To accomplish such hotspots, micro-fluidic cooling was recognized as a promising approach. In light of this, herein, we propose a facile approach of micro-fluidic integration in between stacked dies, which facilitates inter-die cooling. The integration achieved through silicide (Ti/Si) assisted thermo-compression bonding and here, the bonding conditions were optimized by considering the temperature, pressure, surface roughness, and the thickness of deposited titanium films for glass-silicon and silicon-silicon stacks. The reliability assessment of stacked dies was performed using confocal scanning acoustic microscopy, pull test analysis, and cross-sectional field emission scanning electron microscopy (FESEM). The mechanism of titanium diffusion across the bonding interface suggested the requirement of the titanium thickness of two proposed stacking methods, and was studied using FESEM cross-sectional elemental distribution analysis and observed the interface mechanism. Also, we fabricated the successful integration of fine (100 µm) micro channels with a 200 µm pitch across multi stacked layers. © 2020 IOP Publishing Ltd.