Tight ultrafiltration (TUF) membranes with high performance have attracted more and more attention in the separation of organic molecules. To improve membrane performance, some methods such as interface polymerization have been applied. However, these approaches have complex operation procedures. In this study, a polydopamine (PDA) modified MoS2 (MoS2@PDA) blending polyethersulfone (PES) membrane with smaller pore size and excellent selectivity was fabricated by a simple phase inversion method. The molecular weight cut-off (MWCO) of as-prepared MoS2@PDA mixed matrix membranes (MMMs) changes, and the effective separation of dye molecules in MoS2@PDA MMMs with different concentrations were obtained. The addition amount of MoS2@PDA increased from 0 to 4.5 wt %, resulting in a series of membranes with the MWCO values of 7402.29, 7007.89, 5803.58, 5589.50, 6632.77, and 6664.55 Da. The MWCO of the membrane M3 (3.0 wt %) was the lowest, the pore size was defined as 2.62 nm, and the pure water flux was 42.0 L m−2 h−1 bar−1. The rejection of Chromotrope 2B (C2B), Reactive Blue 4 (RB4), and Janus Green B (JGB) in aqueous solution with different concentrations of dyes was better than that of unmodified membrane. The separation effect of M3 and M0 on JGB at different pH values was also investigated. The rejection rate of M3 to JGB was higher than M0 at different pH ranges from 3 to 11. The rejection of M3 was 98.17–99.88%. When pH was 11, the rejection of membranes decreased with the extension of separation time. Specifically, at 180 min, the rejection of M0 and M3 dropped to 77.59% and 88.61%, respectively. In addition, the membrane had a very low retention of salt ions, Nacl 1.58%, Na2SO4 10.52%, MgSO4 4.64%, and MgCl2 1.55%, reflecting the potential for separating salts and dyes of MoS2@PDA/PES MMMs.