Intelligent microporous membranes with excellent water resistance and moisture permeability have a huge market demand owing to their wide applications in personal protection, outdoor equipment and wearable electronics. However, the construction of such high-performance waterproof and moisture-permeable membranes (WBMs) based on a simple preparation process without post-coating treatment presents significant challenges. Herein, we present a simple strategy for constructing a fluorine-free polyethylene terephthalate (PET)-based WBM with a novel composite structure by combining a leaf vein-like nanofibrous substrate membrane and lotus leaf-inspired biomimetic nanofibrous skin using multi-needle electrospinning and heat treatment techniques. Surface hydrophobicity, along with the stable crosslinked structure of PET-based membranes, was achieved by in-suit doping of fluorine-free two-component reactive silicone rubber (PDMS). In addition, the small pore size and high porosity of the composite membranes were regulated by co-assembling PET/PDMS fibers and microspheres with different morphologies and structures. The resulting composite membranes based on substrate membrane-1:3 (BNFM-1:3) achieved excellent waterproof performance of 90.3 kPa, good moisture permeability of 5116 g m−2 d−1, and air permeability of 1.82 mm s−1. The WBMs based on novel composite structures are expected to be applied in various fields because of their ideal comprehensive performance.