Thermophoresis　refers　to　the　motion　of　small　particles　suspending　in　a　fluid　with　non-uniform　temperature　distribution　due　to　the　temperature　gradient　around　the　particle.　Usually,　the　fluid　molecules　coming　from　the　hot　side　carry　more　kinetic　energy　than　those　from　the　cold　side,　which　results　in　a　net　thermophoretic　force　in　the　direction　opposite　to　the　temperature　gradient.　Since　it　was　discovered　more　than　100　years　ago,　thermophoresis　has　been　of　major　importance　in　a　variety　of　applications,　where　it　can　play　either　beneficial　role　or　adverse　role,　including　material　synthesis,　micro-　and　nano-fabrication,　and　environmental　science.　Therefore,　it　is　necessary　to　accurately　evaluate　the　thermophoretic　force.　In　the　present　work,　the　thermophoretic　force　on　nanoparticles　is　examined　in　the　free　molecule　regime　by　using　non-equilibrium　molecule　dynamics　(MD)　simulation.　It　has　been　widely　accepted　that　the　thermophoretic　force　conforms　with　the　Waldmann　equation　for　large　Knudsen　numbers.　However,　due　to　the　effect　of　the　nonrigid-body　interactions　between　the　particle　and　gas　molecules,　the　thermophoretic　force　on　nanoparticles　might　deviate　greatly　from　the　classical　theory.　In　our　MD　model,　a　single　nanoparticle　with　a　diameter　of　several　nanometers　suspends　in　a　diluted　gas.　The　Lennard-Jones　(L-J)　potential　is　employed　to　simulate　the　intermolecular　interactions.　To　avoid　deforming　the　nanoparticle,　the　solid　molecules　within　the　nanoparticles　are　linked　to　their　nearest　neighbors　through　a　finite　extensible　nonlinear　elastic　bonding　potential.　The　thermophoretic　force　on　a　nanoparticle　is　calculated　by　imposing　a　harmonic　potential　on　the　nanoparticle,　which　eliminates　the　effect　of　the　Brownian　motion　of　the　nanoparticle　on　the　thermophoresis.　The　effective　thermal　conductivity　of　the　ambient　gas　is　employed　in　Waldmann　equation　for　the　thermophoretic　force　due　to　the　finite　volume　effect.　It　is　found　that　the　Waldmann　theory　for　thermophoresis　is　still　valid　for　nanoparticles　in　the　case　of　weak　gas-particle　interaction　or　high　gas　temperature.　With　the　increase　of　the　gas-particle　interaction　strength　or　the　decrease　of　the　gas　temperature,　the　Waldmann　theory　is　invalid　due　to　the　effect　of　gas-particle　nonrigid-body　collisions　and　the　adsorption　of　gas　molecules　on　the　particle　surface.　By　considering　the　gas-particle　nonrigid-body　interaction　and　the　modified　particle　size,　the　theoretical　results　for　thermophoretic　force　accord　with　the　MD　simulations　quite　well.