High permeance nanofiltration membranes with an ultra-low molecular weight cut-off (MWCO) in the range of 150–200 g mol−1 and selective towards small solutes are essential for ionic and molecular separation. Despite the market dominance of thin film composite poly(piperazine-amide) nanofiltration membranes, the higher MWCO (>250 g mol−1) limits their widespread applications in molecular-level discrimination. Herein, we report the fabrication of new carbo-cationic microporous poly(triaminoguanidinium-amide) nanofilm composite membranes from an alkaline solution of triaminoguanidinium chloride (TG) and hexane solution of trimesoyl chloride (TMC) via interfacial polymerization. The microporous (mean pore size ∼1.1–1.3 nm) structure of the nanofilm with a thickness down to ∼30 nm allows convective transport of water with permeance as high as 19.0 ± 0.5 L m−2 h−1 bar−1 (at 4 bar), and tunable salt rejection of MgCl2 (21.5–85%), NaCl (41.6–85%) and Na2SO4 (98.7–99.7%) with a high ion selectivity of ∼140 between NaCl and Na2SO4. The membranes exhibit a low MWCO of 163–200 g mol−1 for neutral solutes, low rejection of glycerol (∼32.0%), high rejection of NaCl (∼85%), and excellent stability at low pH. Such ultra-low MWCO membranes would boost their applications in antibiotic removal, desalination, wastewater treatment, and many industrial separation problems concerning separating small neutral solutes.