The processing method for Chinese traditional herbal medicine is "Pao Zhi" in Chinese. This study examined the efficacy of the Pao Zhi on the preparations of Gardeniae Fructus (GF) on a mitochondrial respiratory function in rats. To determine the efficacy of Pao Zhi, we investigated the effects of GF heat processing on mitochondrial respiratory function. To test the GF components, the rats were randomly divided into a geniposide-alone group, crocin-alone group, and combination groups and treated with geniposide and crocin at different ratios. The results showed that a high dose, raw GF was more effective in improving the neurological function, mitochondrial respiratory function, and activities of Na+-K+-ATPase and Ca2+-Mg2+-ATPase than the preparations that underwent heating. Moreover, mitochondrial ROS production was the lowest in the raw GF-treated group. In addition, treatments with crocin and GC3 were more effective than geniposide in improving the functional deficit in MCAO rats. In conclusion, our results suggest that raw GF is the most suitable preparation for the treatment of cerebral ischemia, and its underlying mechanisms may be associated with the improvement of mitochondrial respiratory function, increased activities of Na+-K+-ATPase and Ca2+-Mg2+-ATPase, and reduced oxidative stress in mitochondria. Our findings suggest that raw GF, especially crocin, could be an ideal therapeutic agent for ischemic stroke.