In this paper, a series of silicon hybrid polyurethane‐imides (SPUI) with high stability were constructed by introducing diphenylsilanediol (DPSD) and imidization effect, in which the segment character and hydrogen bonding were adjusted. Various “sea‐island” microphase separations, similar evolution from blooming flower to bud like microdomains was originating from the hard segment clusters, where the segment distribution was labeled and visualized by the stacking of silicon heteroatom. Comparing with pure polyurethane (PU), tensile strength and elongation at break for SPUIs increased from 0.71 ± 0.04 to 17.67 ± 1.84 MPa and from 84.39% ± 6.79% to 202.38% ± 14.50%, respectively. Interestingly, the silicon‐induced aggregates of hard segments in SPUI/graphite flakes (SPUI/GFs), densely crowded around GFs except for some dispersions, revealing similar coupling agent characters of SPUI and self‐affinity with GFs. Thus, the high performance was achieved due to adjustable percolation and cross‐linking networks. Percolation thresholds were decreased from 2.04 to 0.61 wt% and the conductivity of 1.0 × 100 S/m at GFs contents of 5.0 wt% for SPUIz/GFs‐500 was achieved, 2–3 orders of magnitude higher than that of SPUIz/GFs‐2000 except for high stability in conductivity, far lower than those of reported composites. Finally, this study was of great significance for developing functional PU materials with high performance.