This study presents an innovative approach to membrane fabrication through the development of Fe3O4-modified Cs-based mixed matrix membranes, utilizing magnetic-field-assisted nanoparticle orientation and environmentally friendly cross-linking with sodium tripolyphosphate (STP) to enhance isopropanol dehydration performance. This study examines the influence of various preparation parameters—the magnetic field application during fabrication, Fe3O4 nanoparticle content, and the concentration of cross-linking agent sodium tripolyphosphate (STP)—on the membrane structural and functional properties. A comprehensive suite of analytical techniques, encompassing Fourier-transform infrared and nuclear magnetic resonance spectroscopy, X-ray powder diffraction, dynamic light scattering, X-ray photoelectron spectroscopy, scanning electron microscopy with energy-dispersive X-ray spectroscopy, atomic force and transmission electron microscopy, thermogravimetric analysis, differential scanning calorimetry, magnetic measurements, swelling tests, contact angle assessments, and mechanical property evaluations, was employed to validate structure and characteristics of membranes and modifier. Additionally, computational analysis was conducted to elucidate the interactions between membrane and feed components, providing insight into the separation performance. By incorporating an optimal 5 wt% of Fe3O4 into the Cs matrix under a magnetic field, utilizing a porous substrate, and cross-linking with 3 wt% STP, a cross-linked supported membrane demonstrated significantly enhanced transport parameters: 0.13–0.65 kg/(m2 h) permeation flux, ≥ 725 kg/(m2 h) separation index, ≥ 3577 GPU water permeance when isopropanol dehydration (12–90 wt% water). Notably, the membrane exhibited excellent long-term stability under continuous pervaporation for a 14-day period, including at elevated temperatures, indicating its potential for practical applications in dehydration processes.