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3D multi-core architectures are seen to provide increased transistor density, reduced power consumption, and improved performance through wire length reduction. However, 3D suffers from increased power density, which exacerbates thermal hotspots. In this paper, we present a novel 3D multi-core architecture that reduces processor activity on the die distant to the heat sink and a core-level dynamic thermal management technique based on the architectural adaptation, e.g. dynamically adapting core-resources depending on diverse application requirements and thermal behavior. The proposed thermal management technique synergistically combines the benefits of the architectural adaptation supported by our 3D multi-core architecture with dynamic voltage and frequency scaling. Our proposed technique provides 19.4% (maximum 24.4%, minimum 15.5%) improvement in the instruction throughput compared to the state-of-the-art thermal management techniques applied to the thermal-aware 3D processor architecture without considering run-time adaptation.