The crystallization behavior of silica-filled polydimethylsiloxane (PDMS) was investigated in detail by 1H solid-state nuclear magnetic resonance (1H SS-NMR) in combination with synchrotron radiation wide-angle X-ray scattering (WAXS), and temperature-modulated differential scanning calorimetry (TMDSC) techniques. For neat PDMS, no apparent difference is observed for the crystallinity characterized by 1H SS-NMR and WAXS at low-temperature regions. However, upon filler addition, a 15%–35% lower difference in crystallinity is observed measured by 1H SS-NMR compared to WAXS. The origin of such mismatch was explored through multi-component structural, dynamics, and chain-order analysis of PDMS samples with different filler fractions. The 1D integrated WAXS results of PDMS with different filler fractions at different temperatures show that the packing structure as well as crystal size basically remain unchanged, but as the filler fraction increases from 0 phr to 60 phr, the rigid component’s dynamics order parameter Sr obtained by 1H SS-NMR decreases from 0.70 to 0.55. The filler fraction-dependent crystallinity calculated based on Sr was compared with experimental values, revealing a behavior of decreasing order in the crystalline region. Combining with the results of accelerated chain dynamics in crystalline region as reflected by T2 values, the molecular origin is attributed to the formation of CONDIS crystals, whose conformational order is lost but the position and orientation orders are kept. Such hypothesis is further supported by the TMDSC results, where, as the filler fraction increases from 0 phr to 60 phr, the melting range widens from 8.77 K to 14.56 K, representing a growth of 166%. In addition to previous reports related to the condition for forming CONDIS mesophase, i.e., temperature, pressure, and stretching, the nano-sized filler could also introduce the local conformational disorder for chain packing.