Joining table from Linked Server is very slow
Put an index on A.ID  

Add a &lt;> so it can avoid taking locks  

update A
    set A.ColumnA = B.ColumnB
from #Table A
join [LinkedServer].[DB].[dbo].[Table] B 
  on A.ID = B.ID 
where A.ColumnA &lt;&gt; B.ColumnB or A.ColumnA is null