Recent approaches for dynamic thermal management (DTM) of 3D memories demonstrated leakage power to be a significant contributor towards heating in 3D memories and proposed the closing of memory channels as a part of the strategy to keep the temperature within safe operating limits. Since the leakage power of various memory channels is affected by variations in the manufacturing process, there is a need for DTM strategies to be aware of this phenomenon. We propose VarCool, a channel level variability-aware approach for DTM of 3D memories. VarCool is a three-pass strategy that considers temperature, leakage, access rate, and position of various memory channels for DTM. Compared to state-of-the-art, our experiments demonstrate an improvement of up to 31%, 58%, 68% (2%, 15%, 16% on average) in performance, energy, and energy-delay product respectively on different workloads consisting of SPEC CPU2006 benchmarks.