The acid-accepting and gas-generating properties, along with the formation of extensive nanovoids, make CaCO3 nanoparticles attractive as sacrificial nanofillers for fabricating thin-film composite (TFN) nanofiltration membranes. However, challenges such as severe agglomeration and limited acid etching efficiency of the nanoparticles hinder the pursuit of superior membrane performance. In this study, the dispersion and compatibility of CaCO3 nanoparticles within the membrane matrix were improved by modifying them with a polydopamine (PDA) coating. The abundant phenolic hydroxyl groups of PDA enhanced the hydrophilicity and negative charges of membrane surface. Additionally, the PDA capsule increased the etching extent of the CaCO3 nanoparticles by improving the nanoparticle dispersion and generating additional acid, which created sufficient water channels within the polyamide layer. It was demonstrated that incorporating 45 μg/cm2 of PDA-modified CaCO3 nanoparticles doubled the water permeance to 16.7 LMH/bar, while maintaining a low molecular weight cut-off of 249 Da and achieving rejections over 90% for five types of per- and polyfluorinated substances. The PDA modification also overcame the membrane stability issue caused by the agglomerated CaCO3 nanoparticles. This study provides a novel strategy for applying properly modified self-etching nanofillers in TFN membrane development, showing great potential for water treatment applications.