Increasing the C4AF content significantly enhances the sulfate and impact resistance of Portland cement-based materials. However, the research on the microstructural evolution mechanisms and micromechanical properties of the binary synergistic hydration products of C4AF and gypsum is not yet sufficiently deep. This study employed thermodynamic simulations, phase structure characterization, and nanoindentation techniques to investigate the microstructure evolution of gypsum-assisted C4AF hydration. Results indicated that the final hydration product of C4AF, C3(A,F)H6, formed through the stacking of lamellar OH-AFm phases. The addition of gypsum altered the formation pathway of C3(A,F)H6, causing it to precipitate directly from an amorphous iron-aluminum gel, which resulted in smaller particles with higher crystallinity. Gypsum also filled pores in the hydration products, thereby positively influenced their micromechanical properties.