State-of-the-art devices in the consumer electronics market are relying more and more on Multi-Processor Systems-On-Chip (MPSoCs) as an efficient solution to meet their multiple design constrains, such as low cost, low power consumption, high performance and short time-to-market. In fact, as technology scales down, logic density and power density increase, generating hot spots that seriously affect the MPSoC performance and can physically damage the final system behavior. Moreover, forthcoming three-dimensional (3D) MPSoCs can achieve higher system integration density, but the aforementioned thermal problems are seriously aggravated. Thus, new thermal exploration tools are needed to study the temperature variation effects inside 3D MPSoCs. In this paper, we present a novel approach for fast transient thermal modeling and analysis of 3D MPSoCs with active (liquid) cooling solutions, while capturing the hardware-software interaction. In order to preserve both accuracy and speed, we propose a close-loop framework that combines the use of Field Programmable Gate Arrays (FPGAs) to emulate the hardware components of 2D/3D MPSoC platforms with a highly optimized thermal simulator, which uses an RC-based linear thermal model to analyze the liquid flow. The proposed framework offers speed-ups of more than three orders of magnitude when compared to cycle-accurate 3D MPSoC thermal simulators. Thus, this approach enables MPSoC designers to validate different hardware- and software-based 3D thermal management policies in real-time, and while running real-life applications, including liquid cooling injection control