In response to the urgent demand for high performance microwave composite substrates for high power devices, high density packaging and other microwave communication fields, a new technique combining twin-screw pelletizing and hot press molding is proposed to prepare high thermal conductivity microwave composite substrates with high anti-impact polystyrene (HIPS) as the matrix and hexagonal boron nitride (h-BN) ceramics as the filler. The microstructure, microwave dielectric properties and thermal properties of the substrates are fully characterized. The results show that the use of h-BN25 with a large particle size of 25 μm is more beneficial than h-BN5 with a small particle size of 5 μm in improving the thermal conductivity λ and reducing the dielectric loss tan δ. As the filling ratio w of h-BN25 increases from 0 to 70%, the thermal conductivity of the HIPS/ h-BN25 microwave composite substrate increases from 0.13 W·m-1·K-1 to 7.43 W·m-1·K-1(in-plane) and 2.55 W·m-1·K-1 (inter-plane), which are 57 and 20 times higher than that of-pure HIPS, respectively, indicating that the above-mentioned preparation technique can realize the directional arrangement of h-BN in the HIPS matrix and build an effective in-plane thermal conductivity network. Meanwhile, the dielectric loss tan δ of the composite substrate is reduced from 7.3×10-4 to 5.3×10-4 (10 GHz), the coefficient of thermal expansion α is reduced from 93.8×10-6/K to 18.7×10-6/K. The HIPS/ h-BN25 microwave composite substrate filled with 70% of h-BN25 ceramic has excellent comprehensive performance, the thermal conductivity λ=7.43 W·m-1·K-1, dielectric constant εr=3.9, dielectric loss tan δ=5.3×10-4 and the coefficient of thermal expansion α=18.7×10-6/K at 10 GHz, which exhibits good application prospects in the field of microwave communication.