A key challenge for three dimensional (3D) integrated circuits (ICs) is thermal management. There are two main thermal challenges in typical 3D ICs. First, in the homogeneous integration with multiple high-power tiers, an effective cooling solution that scales with the number of dice in the stack is needed. Second, in the heterogeneous integration, an effective thermal isolation solution is needed to ‘protect’ the low-power tier from the high-power tier. This research focuses to address these two thermal challenges through hybrid microfluidic cooling and thermal isolation technologies. Within-tier microfluidic cooling is proposed and demonstrated to cool a stack with multiple high-power tiers. Electrical thermal co-analysis is performed to understand the trade-offs between through silicon via (TSV) parasitics and heat sink performance. A TSV-compatible micropin-fin heat sink is designed, fabricated and thermally characterized in a single tier, and benchmarked with a conventional air-cooled heat sink. The designed heat sink has a thermal resistance of 0.269 K·cm2/W at a flow rate of 70 mL/min. High aspect ratios TSVs (18:1) are integrated in the micropin-fins. Within-tier microfluidic cooling is then implemented in 3D stacks to emulate different heating scenarios, such as memory-on-processor and processor-on-processor. Air gap and mechanically flexible interconnects (MFIs) are proposed for the first time to decrease the vertical thermal coupling between high-power (e.g. processor) and low-power tiers (e.g. memory or nanophotonics). A two-tier testbed with the proposed thermal isolation technology is designed, fabricated and tested. Compared with conventional 3D integration approach, thermal isolation technology helps reduce the temperature at a fixed location in the low-tier by 12.9 °C. The resistance of a single MFI is measured to be 46.49 mΩ.