Molecular dynamics (MD) simulation was employed to predict the thermal conductivity of poly(dimethylsiloxane) (PDMS)/hexagonal boron (h-BN) composite. Two MD simulation models were constructed. Model one is h-BN monolayer being adsorbed by PDMS chains, which is designed to examine the influence mechanism of polymer molecules on the heat conduction of h-BN. The polymer molecules were divided into several layers along the normal direction of the h-BN, which had different impacts on the thermal conductivity of h-BN. Model two is PDMS composites with different volume fractions of h-BN monolayer, which is used to investigate the influence of h-BN on thermal conductivity of the composites. Meanwhile, the orientation of the h-BN under the oscillatory shear was also considered. It presents three regimes on the thermal conductivity increased with the packing fraction after shearing. In general, this work opens some insightful avenues for manipulating the thermal conductivity of PDMS/h-BN composite.