3D stacked architectures are getting increasingly attractive as they improve yield, reduce interconnect power and latency, and enable integrating layers manufactured with different technologies on the same chip. However, 3D integration results in higher temperatures following the increase in thermal resistances. This chapter discusses thermal modeling and management of 3D systems with a particular focus on liquid cooling, which has emerged as a promising solution for addressing the high temperatures in 3D systems. We first introduce a framework that is capable of detailed thermal modeling of the interlayer structure containing microchannels and through-silicon-vias (TSVs). For energy-efficient liquid cooling, we describe a controller to adjust the liquid flow rate to meet the current chip temperature. We also discuss job scheduling techniques for balancing the temperature across the 3D system to maximize the cooling efficiency and to improve reliability.