The excellent performance and wide applications of phenyl polysiloxanes are largely due to their phenyl units and monomer sequences. However, the relationship between molecular structure and material properties has not been explicitly elucidated. In this work, the sequence distribution and microstructure of random copolymers were quantitatively investigated by means of a molecular dynamics (MD) simulation combined with experimental verification. The results of 29Si NMR showed that the large number of phenyl units not only shortened the length of the dimethyl units, but also significantly increased the proportion of consecutive phenyl units. The simulation results indicated the attraction between adjacent phenyl groups that were effectively strengthened intra- and inter- molecular interactions, which determined the equilibrium population of conformations and the dynamics of conformational transitions. Furthermore, the evolution of bond angle distribution, torsion distribution, and mean-squared displacements (MSD) shed light on the conformational characteristics that induce the unique thermodynamics properties and photophysical behavior of high-phenyl polysiloxanes. Differential scanning calorimetry (DSC), dynamical mechanical analysis (DMA), spectrofluorimetry, and laser scanning confocal microscopy (LSCM) were performed to verify the conclusions drawn from the simulation. Overall, the complementary use of MD simulations and experiments provided a deep molecular insight into structure–property relationships, which will provide theoretical guidance for the rational design and preparation of high-performance siloxanes.