Abstract The microstructures of fluorinated polyurethanes (FPUs) possess separated soft and hard phases related to their unique mechanical and physiochemical properties. We studied the microstructures of FPUs and H-bond interactions focusing on the influences of fluorine (F) content on the separation between the soft and hard phases by combining experimental and computational approaches. FPUs featuring F in side chains were synthesized using fluorinated polyether glycol as soft segments, MDI as hard segments, and 1,4-butanldiol (BDO) as chain extenders with various molar ratio of hard/soft segments. Fourier transform infrared spectroscopy (FTIR) and molecular dynamics (MD) studies both show that increasing F content of soft segments enhances H-bond interactions between soft and hard segments, thus reducing the extent of microphase separation. The direct visual inspection of microstructures by SEM reveals that the soft and hard segments separate more significantly as the fraction of the hard segments increases, consistent with the increasing density fluctuation of F and N elements found in the MD simulations. The glass transition temperatures (Tg) measured by DMA indicate that the optimal working temperature window of FPUs separating soft and hard glass transitions becomes narrow with increasing F and weakened phase separation. Tg predicted by MD are in quantitative agreement with the DMA experiments. This work demonstrates that how experiments and computations can be combined to study composition-structure-property relationships of polymers to optimize the separated microphase structures of FPU for overall good balance among materials performance, synthesis costs, and environmental impacts.