Polysiloxanes are known to significantly enhance the toughness and thermal stability of epoxy resins. However, the study of phase transitions and their effects on the properties of modified resins, synthesized through copolymerization or blending, was quite limited. In this work, a phenyl propyl polysiloxane (PPPS) modified epoxy resin (P/E) was prepared using a solvent method to scrutinize the influence of varying PPPS concentrations and phase transitions on the macroscopic properties of the resin. The molecular structure of P/E composite was confirmed through Fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (1H and 29Si NMR) analysis. Based on atomic force microscopy (AFM) results, the progression of phase transitions was deduced: from a homogeneous phase to a co-continuous phase, and subsequently to a sea-island phase. This progression of phase transitions is attributed to the varying solubility of the copolymer with different PPPS content in the resin. At a PPPS content of 20 wt%, a significant improvement in tensile strength (σ) and critical strain energy release rate (GIc) was observed, increasing by 45 % and 400 %, respectively, upon the formation of a co-continuous phase. The presence of a silicone-rich spherical domain within sea-island phase can significantly improve the GIc of the resins, while this also results in a rapid reduction in tensile strength (σ). Furthermore, the thermal stability of P/E composite is also affected by its phase structures. The silicone-rich spherical domains are more effective in forming a protective layer compared to the co-continuous phase, which leads to a decreased pyrolysis rate and an increased yield of residual char. This work elucidates the influence of PPPS content and phase structure on the macroscopic properties, highlighting the significant potential for developing composite materials with superior comprehensive performance.