Copper　filled　through　silicon　via　(TSV-Cu)　is　a　crucial　technology　for　chip　stacking　and　three-dimensional　(3D)　vertical　packaging.　The　multiple　thermal　loadings　caused　by　the　annealing　process　and　deposition　of　interconnected　dielectric　layers　lead　to　continuous　TSV-Cu　protrusions,　which　can　affect　its　reliability　severely.　In　this　paper,　the　relationship　between　second　protrusion　height　of　TSV-Cu　and　its　microstructur　characteristics　during　double　annealing　is　quantitatively　investigated.　It　is　found　that　grain　size　of　TSV-Cu　after　annealing　once　is　larger,　and　the　second　protrusion　value　under　additional　annealing　can　be　greatly　reduced.　The　reduction　phenomenon　of　second　protrusion　is　relative　to　the　microstructure　characteristics　such　as　＜111＞　texture　and　Sigma　3　grain　boundary　type.　In　addition,　stress　and　strain　are　analyzed　by　finite　element　analysis　(FEA)　to　reveal　the　reduction　mechanisms　of　the　second　protrusion　height　of　TSV-Cu　during　double　annealing.　The　initial　residual　stress　of　fabricated　TSV-Cu　and　its　mechanical　property　parameters　measured　by　nanoindentation　test　are　incorporated　in　FEA.　The　main　results　show　that　additional　thermal　loading　leads　to　a　smaller　increase　of　equivalent　plastic　strain　(PEEQ)　and　von　Mises　stress　if　the　TSV-Cu　is　annealed　firstly　at　a　high　temperature　of　400　degrees　C.　This　verifies　the　second　protrusion　tendency　of　TSV-Cu,　and　explains　the　reduction　mechanisms　of　the　second　protrusion　height　of　TSV-Cu.