Si/Ge superlattices are promising thermoelectric materials to convert thermal energy into electric power. The nanoscale thermal transport in Si/Ge superlattices is investigated via molecular dynamics (MD) simulation in this short communication. The impact of Si and Ge interface on the cross-plane thermal conductivity reduction in the Si/Ge superlattices is studied by designing cone-structured interface and aperiodicity between the Si and Ge layers. The temperature difference between the left and right sides of the Si/Ge superlattices is set up for nonequilibrium MD simulation. The spatial distribution of temperature is recorded to examine whether the steady-state has been reached. As a crucial factor to quantify thermal transport, the temporal evolution of heat flux flowing through Si/Ge superlattices is calculated. Compared with the even interface, the cone-structured interface contributes remarkable resistance to the thermal transport, whereas the aperiodic arrangement of Si and Ge layers with unequal thicknesses has a marginal influence on the reduction of effective thermal conductivity. The interface with divergent cone-structure shows the most excellent performance of all the simulated cases, which brings a 33% reduction of the average thermal conductivity to the other Si/Ge superlattices with even, convergent cone-structured interfaces and aperiodic arrangements. The design of divergent cone-structured interface sheds promising light on enhancing the thermoelectric efficiency of Si/Ge based materials.