是什么使Tom变成现在这个样子.
it is that 强调句型,在这里强调what,“什么”,强调句型在句中不做成分,可以不看它,这样句子就变成了：what has made Tom what he is now.
然后 第一个 what 做主语 has made 是谓语 Tom 是宾语
what he is now 是从句做宾补,在这里what做系动词is的宾语,主语是he,now 是时间状语.