3D stacked architectures reduce communication delay in multiprocessor system-on-chips (MPSoCs) and allowing more functionality per unit area. However, vertical integration of layers exacerbates the reliability and thermal problems, and cooling is a limiting factor in multi-tier systems. Liquid cooling is a highly efficient solution to overcome the accelerated thermal problems in 3D architectures. However, liquid cooling brings new challenges in modeling and run-time management. This paper proposes a design-time/run-time thermal management policy for 3D MPSoCs with inter-tier liquid cooling. First, we perform a design-time analysis to estimate the thermal impact of liquid cooling and dynamic voltage frequency scaling (DVFS) on 3D MPSoCs. Based on this analysis, we define a set of management rules for run-time thermal management. We utilize these rules to control and adjust the liquid flow rate in order to match the cooling demand for preventing energy wastage of overcooling, while maintaining a stable thermal profile in the 3D MPSoCs. Experimental results on multi-tier 3D MPSoCs show that proposed design-time/run-time management policy prevents the system to exceed the given threshold temperature while reducing cooling energy by 50% on average and system-level energy by 18% on average in comparison to using a static worstcase flow rate setting.