Objective To compare the transparency efficiency of six different optical clearing method on the rat brain tissues. Methods Brain tissue blocks of 14 SD rats were processed with iDISCO, SeeDB, CUBIC, SCALEVIEW-A2, CLARITY-CUBIC, Passive-CLARITY clearing method, respectively. Results The gray value of PBS group was 13.031 ±0.586, that of iDISCO, SeeDB, CUBIC, SCALEVIEW-A2, CLARITY-CUBIC, passive-CLARITY clearing were 6.447 ±0.574, 11.690 ±0.909, 2.318 ±0.986, 8.118 ±1.026, 8.591 ±0.384, 4.198 ±0.182, respectively. Except the SeeDB group ( P =0.185), the rest groups showed significant differences compared with the PBS group ( P < 0.01), and there were significant differences between CUBIC and other groups ( P < 0.01). After the clearing treatment, the changes of tissue area ratio in the iDISCO, SeeDB, CUBIC, SCALEVIEW-A2, CLARITY-CUBIC, Passive-CLARITY method were( -30.02 ±2.39)%,(19.74 ±4.09)%,(14.7 ± 3.92)%,(10.7 ± 5.55)%,(23.01 ± 4.19)%,(66.51±5.68)%, respectively. Each group showed a significant difference compared with the groups iDISCO and the Passive-CLARITY, P < 0.01. Conclusions Except the SeeDB method, all the clearing methods can achieve a transparent effect, while CUBIC is better than the other groups applied for rat brain tissues. The tissue block volume is shrunken after iDISCO clearing, and expanded after Passive-CLARITY processing.