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A co-polymer (SPAA6) of 5-sulfoanthranilic acid (5SAA) and e-caprolactam was used to prepare membrane through nonsolvent induced phase separation (NIPS) method. The micro-structure of membrane was adjusted by small molecules to improve mechanic strength and performance, involving 7 commercial ionic surfactant and a self-synthesized one, S20. S20 showed the best compatibility with SPAA6, which converted spherical phase into network of strip-like units in micro-structure of membrane. Meanwhile, average pore size of the membrane was narrowed from 4.271 nm to 3.391 nm, tested by BET method. Tensile strength of membrane was improved from 2.5 MPa to 2.9 MPa. Therefore, anionic dyes rejection and membrane stability were both improved. It actually demonstrated that molecular weight distribution of SPAA6 was crucial for micro-structure construction of membrane since S20 was the SPAA6 of low molecular weight. In blend solution filtration test, membrane MS2 (1:2 for S20:SPAA6) displayed 98.22% rejection to Congo Red (CR) acid and 96.18% NaCl permeation under 1 bar. It showed 80.18% rejection to chrome blue K (ABK) and 96.28% NaCl permeation. Both water permeance were higher than 3.5 L·m−2·h−1·bar. Membrane MS2 showed the potential of fractionation of dye and NaCl, which was promising in textile waste water treatment.