The demand for waterproof leather has been increasing, and environmentally friendly waterproof fatliquors have recently received increasing attention. In this work, two polymer nanoemulsions containing carboxyl groups were synthesized and used as waterproof fatliquors for chrome-tanned leather. First, a reactive emulsifier (C12-Na) was prepared using itaconic anhydride and lauryl alcohol. Subsequently, two polymer nanoemulsions were prepared through mini-emulsion polymerization with C12-Na as the emulsifier, 4,4′-azobis (4-cyanovaleric acid) as the initiator, and lauryl acrylate (LA)/stearyl acrylate (SA) as monomers; these were named PLA and PSA. PLA and PSA were characterized using FT-IR, a Zetasizer, and GPC. It was found that the critical micellar concentration (CMC) of C12-Na was 2.34 mmol/L, which could reduce the surface tension of water to 26.61 mN/m. The average particle sizes of PLA and PSA were 53.39 and 67.90 nm, respectively. The maeser flexes of leather treated with PLA and PSA were 13928 and 19492 at a 5% dosage, respectively, and the contact angles reached 148.4° and 150.3°, respectively; these values were both higher than for a conventional fatliquor. Compared with PLA, the leather treated with PSA exhibited better fullness, and tensile and tearing strength. The prepared nanoemulsions have prospective applications in leather manufacturing as waterproof fatliquors.