A system and a method for treating salt-containing glycerin wastewater are provided, wherein the system for treating the salt-containing glycerin wastewater includes a mixing tank, a filtering device, a distillation column, and a water supply device. The mixing tank is adapted to mix salt-containing glycerin wastewater with a concentrated hydrochloric acid to obtain a mixture. The filtering device communicates with the mixing tank and filters the mixture to obtain an acidic filtrate and a precipitated salt. The distillation column communicates with the filtering device and receives the acidic filtrate from the filtering device. The water supply device supplies water to the acidic filtrate. The system and method for treating the salt-containing glycerin wastewater can effectively recycle hydrochloric acid.