Copper clad laminates (CCLs) with low dissipation factor (Df) are urgently needed in the fields of high-frequency communications devices. A novel resin matrix of modified poly (2,6-dimethyl-1,4-phenylene ether) (MPPE) and styrene-ethylene/butylene-styrene (SEBS) was employed in the fabrication of high-frequency copper clad laminates (CCLs). The composites were reinforced by E-glass fabrics, which were modified with phenyltriethoxysilane (PhTES). The composite laminates obtained exhibited impressive dielectric loss of 0.0027 at 10 GHz when the weight ratio of MPPE to SEBS was 5:1. In order to modify the dielectric constant (Dk), coefficient of thermal expansion (CTE) and other performances of laminates, Li2TiO3 (LT) ceramic powders were introduced into the resin matrix. The composite laminates showed low dielectric loss of 0.0026 at 10 GHz and relatively high flexural strength of 125 MPa when the mass ratio of LT fillers to resin is 0.4. Moreover, the composite laminates all maintain low water uptake (<0.5%). The microstructure and thermal properties of composite laminates filled with LT ceramic powders were also tested. These results show that copper clad laminates prepared with modified polyphenylene ether (MPPE)/SEBS and LT ceramic fillers have strong competitiveness to fabricate printed circuit boards (PCBs) for high-frequency and high-speed applications.