By using through-silicon-vias (TSV), three dimension integration technology can stack large memory on the top of cores as a last-level on-chip cache (LLC) to reduce off-chip memory access and enhance system performance. However, the integration of more on-chip caches increases chip power density, which might lead to temperature-related issues in power consumption, reliability, cooling cost, and performance. An effective thermal management scheme is required to ensure the performance and reliability of the system. In this study, a fuzzy-based thermal management scheme (FBTM) is proposed that simultaneously considers cores and stacked caches. The proposed method combines a dynamic cache reconfiguration scheme with a fuzzy-based control policy in a temperature-aware manner. The dynamic cache reconfiguration scheme determines the size of the cache for the processor core according to the application that reaches a substantial amount of power consumption savings. The fuzzy-based control policy is used to change the frequency level of the processor core based on dynamic cache reconfiguration, a process which can further improve the system performance. Experiments show that, compared with other thermal management schemes, the proposed FBTM can achieve, on average, 3 degrees of reduction in temperature and a 41% reduction of leakage energy.