We propose efficient algorithms to construct a low-power clock tree for through-silicon-via (TSV)-based 3D-ICs. We use shutdown gates to save clock trees' dynamic power, which selectively turn off certain clock tree branches to avoid unnecessary clock activities when the modules in these tree branches are inactive. While this clock gating technique has been extensively studied in 2D circuits, its application in 3D-ICs is unclear. In 3D-ICs, a shutdown gate is connected to a control signal unit through control TSVs, which may cause placement conflicts with existing clock TSVs in the layout due to TSV's large physical dimension. We develop a two-phase clock tree synthesis design flow for 3D-ICs: (1) 3D abstract clock tree generation based on K-means clustering and (2) clock tree embedding with simultaneous shutdown gates' insertion based on simulated annealing (SA) and a force-directed TSV placer. Experimental results indicate that (1) the K-means clustering heuristic significantly reduces the clock power by clustering modules with similar switching behavior and close proximity, and (2) the SA algorithm effectively inserts the shutdown gates to a 3D clock tree, while considering control TSV's placement. Compared with previous 3D clock tree synthesis techniques, our Kmeans clustering-based approach achieves larger reduction in clock tree power consumption while ensuring zero clock skew.