The present research aimed to investigate the influence of layer arrangement and composition ratio on tensile and transport properties in bi-constituent electrospun nanofibrous membranes composed of polyurethane nanofibers with a hydrophobic nature and poly(2-acrylamido-2-methylpropanesulfonic acid) with a hydrophilic nature. Different hybrid electrospun nanofibrous membranes were produced based on different layer arrangement and composition ratios. To evaluate the membrane performance, their tensile strength, wind, and waterproof performance were measured. By adding 50% poly(2-acrylamido-2-methylpropanesulfonic acid) to polyurethane, the pore size of the hybrid electrospun nanofibrous membranes decreased by 47.64%. As a result, compared with pristine polyurethane membranes, hybrid electrospun nanofibrous membranes showed a good (9.6 mm s−1) windproof performance. Adding poly(2-acrylamido-2-methylpropanesulfonic acid) nanofibers to the polyurethane resulted in a decrease in mechanical properties and waterproof performance. The results show that the volume fraction of the poly(2-acrylamido-2-methylpropanesulfonic acid) and the electrospinning scenarios have a great influence on the mechanical properties of the samples. The results also show that the mechanical properties of hybrid electrospun nanofibrous membranes can be predicted based on the geometrical properties of each component. Computational fluid dynamics were used to simulate air flow through a virtual medium and the results of simulation were compared with the experimental measurement and predicted permeability; then, the best models for predicting air permeability were determined. In addition, based on different types of use, duration of use, and relative humidity level, a bi-functional membrane can be obtained by regulating layer arrangement and composition ratios to suit various applications, for example, in medical disposable clothing, wound dressing, filtering industries, and protective clothing.