Nonvolatile memory such as magnetic RAM (MRAM) offers high cell density and low leakage power while suffering from long write latency and high write energy, compared with SRAM. 3-D integration technology using through-silicon vias enables stacking disparate memory technologies (e. g., SRAM and MRAM) together onto chip-multiprocessors (CMPs). The use of hybrid memories as an on-chip cache can take advantage of the best characteristics that each technology offers. However, the inherent high power density and heat removal limitation in 3-D integrated circuits may incur temperature-related problems. In this paper, we propose a runtime thermal management method for CMPs with the 3-D stacked hybrid SRAM/MRAM L2 cache. The proposed method combines dynamic cache management such as resource allocation, way-based power gating, and data migration with dynamic voltage and frequency scaling of processing cores in a temperature- and energy-aware manner. Experimental results show that the proposed runtime method with the 3-D stacked hybrid L2 cache offers up to 107.37% (55.28% on average) performance improvement and 88.47% (47.65% on average) energy efficiency improvement compared with existing thermal management methods with 3-D stacked SRAM-based L2 cache.