Waterproof breathable functional membranes have broad application prospects in the field of outdoors textiles. The fluorine-containing microporous membranes of the mainstream functional products easily cause harm to the environment, and thus, the fluorine-free environmental nanofibrous membranes are an important development direction for functional membranes. In this subject, the electrospun polyacrylonitrile nanofibrous membranes were first hydrophobically modified by amino functional modified polysiloxane (AMP), followed by in situ cross-linking modified with 4, 4'-methyl diphenylene diisocyanate (MDI). The fluorine-free modification by AMP altered the surface of the membranes from hydrophilic to hydrophobic, and greatly improved the waterproof properties with the hydrostatic pressure reaching to 87.6 kPa. In addition, the formation of bonding points and the in situ preparation of polyuria through the reaction between the isocyanate in MDI and the amino group in AMP, could improve the mechanical properties effectively. When using AMP with the concentration of 1 wt% and MDI with the concentration of 2 wt%, the relatively good comprehensive performance was obtained with good water resistance (93.8 kPa), modest vapor permeability (4.7 kg m-2 d-1) and air permeability (12.7 mm/s). Based on these testing data, the modified nanofibrous membranes had excellent waterproof and breathable properties, which has future potential in outdoor sports apparel.