Improving the thermal conductivity (TC) of epoxy resin thermal interface material is of great significance in tackling the heat dissipation problem of high heat flux in microelectronic chips such as 5G. Using non-equilibrium molecular dynamics (MD) method, the effects of two different filling styles of nano-diamond fillers on the TC of EP based composites are investigated. The results show that the TC of the composite increases with the diamond size when single-particle filling is used, and that a larger diamond size leads to a more significant reduction of the free volume fraction and thus an improvement of the TC. In the multi-particle packing, the composite TC first increases and then decreases with increasing particle number. Increasing the number of particles reduces the free volume fraction, but also results in a larger specific surface area and interfacial thermal resistance, which has a more significant weakening effect on the TC. Moreover, within the same mass fraction of nano-diamond filler, increasing the filler size has a more significant TC improvement on the composite than increasing the number of particles. This study is instructive for the design and preparation of high thermal conductivity nanodiamond/epoxy resin composites.