他多年以来做的那个梦在那时结束了.
the dream 是主语
The dream (that) he had had for so many years ended there 省略了that,这里(that) he had had for so many years 是定语从句,因为后面有表示期限的for many years,所以用完成时,而后面ended是过去式,所以用过去完成时
had done 第一个had是助动词,第二个是have的过去分词