The　thermophoresis　of　nanoparticles　suspended　in　gas　is　investigated　in　the　transition　regime　by　molecular　dynamics　simulations.　It　is　found　that　there　exists　significant　discrepancy　between　the　simulation　results　and　the　theoretical　predictions　for　the　thermophoretic　force,　which　is　attributed　to　the　adsorption　of　gas　molecules　on　nanoparticles　and　the　gas-particle　non-rigid　body　collisions.　By　using　the　effective　particle　radius,　the　simulation　results　and　Talbot　et　al.＇s　equation　could　agree　with　each　other　in　the　transition　regime.　In　addition,　the　effect　of　the　finite　system　size　of　the　molecular　dynamics　simulations　is　non-negligible,　and　the　simulation　results　modified　by　effective　particle　radius　can　coincide　with　Phillips＇　equation　quite　well.　Therefore,　for　particles　of　a　few　nanometers,　the　non-rigid　body　collision　effect　and　the　adsorption　of　gas　molecules　and　the　effective　radius　of　the　nanoparticle　under　strong　gas-particle　coupling　should　be　taken　into　account　in　the　theoretical　model.　The　investigation　presented　in　this　paper　provides　guidance　for　the　application　of　nanoparticles　in　aerosol　science.