In　friction　stir　welding　(FSW),　many　defects　(such　as　kissing　bond,　incomplete　penetration,　and　weak　connection)　easily　occur　at　the　root　of　the　welded　joint.　Based　on　the　Levy–Mises　yield　criterion　of　the　Zener–Hollomon　thermoplastic　constitutive　equation,　a　3D　thermal–mechanical　coupled　finite　element　model　was　established.　The　material　flow　behavior　and　the　stress　field　at　the　root　area　of　a　6　mm　thick　2024-T3　aluminum　alloy　FSW　joint　were　studied.　The　influence　of　pin　length　on　the　root　flaw　was　investigated,　and　the　formation　mechanism　of　the　“S　line”　defects　and　non-penetration　defects　were　revealed.　The　research　results　showed　that　the　“S　line”　defect　forms　near　the　bottom　surface　of　the　pin　owing　to　the　insufficiently　mixed　material　from　the　advancing　side　(AS)　and　retreating　side　(RS)　near　the　weld　center.　The　non-penetration　defect　forms　near　the　bottom　surface　of　the　workpiece　owing　to　the　insufficient　driving　force　to　make　the　material　flow　through　the　weld　center.　With　the　continual　increase　of　pin　length,　the　size　of　the　“S　line”　defect　and　non-penetration　defect　reduces,　and　finally,　the　defect-free　welded　joint　can　be　obtained　with　an　optimized　suitable　length　of　the　pin　in　this　case.　©　2020　by　the　authors.　Licensee　MDPI,　Basel,　Switzerland.