A novel process of vortex settling and stage-2 ultrafiltration (UF) with alternating feed direction was used to further concentrate the concentrate produced by a stage-1 UF employed for treatment of banknote printing works wastewater. In this post-treatment process, the final concentrate volume for incineration was reduced by 4-5 times while the permeate of the stage-2 UF could be further reused in the banknote printing operation. It was noted vortex settling facilitated settling of the printing ink and the strategy of regularly alternating feed direction in the UF resulted in a higher permeate flux compared to the corresponding flux for operation without alternating feed direction. The hydraulic retention time (HRT) of the vortex settling tank (VST) used in the pilot-scale experiment was 14 min while feed direction to the stage-2 UF was alternated once every hour. Based on the pilot-scale experimental results, a full-scale system was set up. An economic analysis showed that the novel system was a cost-effective option for post-treatment of stage-1 UF concentrate. The treatment system has been successfully implemented at several Chinese banknote printing companies.