Because the increasing power density is limited by the thermal constraint, multi-core integrated systems have stepped into the dark silicon era recently, meaning not all parts of the system can be powered on at the same time. Dark silicon effects are, especially severe for 3-D microprocessors due to the even higher power density caused by the stacked structures, which greatly limit the system performances. In this article, we propose a greedy based core-cache co-optimization algorithm to optimize the performance of 3-D microprocessors in dark silicon at runtime. The new method determines many runtime settings of the 3-D system on the fly, including the active core and cache bank positions, active cache bank number, and the voltage/frequency (V/f) level of each active core, which optimizes the performance of the 3-D microprocessor under thermal constraint. Because the core-cache settings are co-optimized in the 3-D space and the power budgets are computed dynamically according to the running state of the 3-D microprocessor, the new method leads to a higher system performance compared with the existing methods. Experiments on two 3-D microprocessors show the greedy-based core-cache co-optimization algorithm outperforms the state-of-the-art 3-D dark silicon microprocessor performance optimization method by achieving a higher processing throughput with guaranteed thermal safety.