The anion exchange (AIX) spent brine, generated during the NDMP-3 resin regeneration process, highly loaded with organic substances mainly humic substances (HSs) and salts (mainly NaCl) remains an environmental concern. In this study, pilot-scale electro dialysis (ED) and ultrafiltration (UF) hybrid technologies were first used to recover NaCl solution as a resin regeneration agent and HSs, which could be utilized as a vital ingredient of organic fertilizer, from the AIX spent brine. Recovered ≈ 15% w/w NaCl solution obtained by two-stage pilot-scale ED can be used to regenerate saturated NDMP-3 anion exchange resins; the regeneration–readsorption performance of NDMP-3 resins was equivalent to that of fresh ≈ 15% w/w NaCl solution. The two-stage dilute solution with low-salt content (0.49% w/w) was further concentrated by pilot-scale UF, so that the HS content in the retentate solution was >30 g/L, which meets the HS content required for water-soluble organic fertilizers. The HS liquid fertilizer could significantly stimulate the growth of green vegetables with no phytotoxicity, mainly due to special properties of HSs. These results demonstrate that ED + UF hybrid technologies can be a promising approach for the sustainable treatment and resource recovery of AIX spent brine.