In our previous study, we used optical coherence tomography (OCT) and reported an increase in signal intensity of depth profiles between euthanasia injection and cardiac arrest (CA), demonstrating the potential as a tool for monitoring/diagnosing brain tissue viability [Appl. Opt.48, 4354 (2009)]. Here, for the first time to our knowledge, we measured three-dimensional (3D) OCT images through a thinned skull changing temperatures in the rat brain. The measurements were made at 10 min intervals for 210 min to evaluate correlations of temperature with heart rate and ratios of signal intensity (RSI). The 3D image area was 4 mm × 4 mm × 2.8 mm. When the temperature was decreased from 28°C to 18°C to reduce tissue viability, the heart rate was found to decrease with an increase in RSI. Negative correlation coefficients (CCs) between temperatures and RSIs, and between heart rate and RSIs, were obtained. This indicates that OCT signals increase with reductions of viability caused by decreases in heart rates and temperatures in tissues. These observations correspond to estimations obtained by multiwavelength diffuse reflectance spectroscopy [Appl. Opt.47, 4164 (2008)]. CCs and stationary RSIs would depend upon measured positions in tissues. Without injections for euthanasia, a similar rapid increase in RSI has also been measured before CA.