3D integration of multiple active layers into a single chip is a viable technique that greatly reduces the length of global wires by providing vertical connections between layers. However, dissipating the heat generated in the 3D chips possesses a major challenge to the success of the technology and is the subject of active current research. Since the generated heat degrades the performance of the chip, thermally insensitive/adaptive circuit design techniques are required for better overall system performance. In this paper, we propose a thermally adaptive 3D clocking scheme that dynamically adjusts the driving strengths of the clock buffers to reduce the clock skew between terminals. We investigate the relative merits and demerits of two alternative clock tree topologies in this work. Simulation results demonstrate that our adaptive technique is capable of reducing the skew by 61.65% on the average, leading to much improved clock synchronization and design performance in the 3D realm.