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We propose 3D mesh-based optical network-on-chip (ONoC) based on a novel low-cost 6×6 optical router, and quantitatively analyze thermal effects on the 3D ONoC. Evaluation results show that with the traditional thermal tuning technique using microheater, the average power efficiency of the 3D ONoC is about 2.7pJ/bit, while chip temperature varies spatially between 55°C and 85°C. In comparison, a new technique using the optimal device setting can improve the average power efficiency to 2.1pJ/bit. It is shown that in this particular case, the effectiveness of the two techniques is comparable. If we apply both techniques at the same time, the average power efficiency can be further improved to 1.3pJ/bit.