Cistanche deserticola is a valuable Chinese herb, but traditional dry processing causes the loss of active substances. This study developed Cistanche deserticola fermented juice (CFJ) using lactic acid bacteria and optimized the fermentation process to achieve the maximum active substance content and taste. More interestingly, superoxide dismutase (SOD) activity was increased during fermentation, and CFJ exerted a reparative effect on ethanol-induced cell damage. SOD activity reached 603.26 U/mL when the ratios in the total inoculum volume of Lactobacillus reuteri, Lactococcus pentosus, Streptococcus thermophilus, Bifidobacterium animalis, Lactobacillus casei, and Lactobacillus acidophilus were 31.74%, 15.71%, 17.45%, 11.65%, 9.56%, and 13.89%, respectively. Further, the optimal fermentation conditions for CFJ were determined using a response surface methodology. More importantly, CFJ promoted the proliferation of WRL68 cells, and CFJ exerted an obvious reparative effect on ethanol-treated cells, in which the cell survival rate increased to 120.35 ± 0.77% (p < 0.05). The underlying mechanism might have been that CFJ reduced the MDA content in damaged cells from 1.36 nmol/mg prot to 0.88 nmol/mg prot and increased GSH-Px and SOD activities by 48% and 72%, respectively. This study provides a theoretical basis and reference data for the fermentation of C. deserticola and its hepatoprotective activity.