He is the best student that I have seen这句的先行词是the best student 然后因为有the best*修饰所以用that 这样理解可以吗?

对的 如果先行词被序数词或形容词*修饰时，定语从句的关系代词只能用that，先行词student有the best形容词*修饰，故用that~

这样理解完全正确.

定语从句中关系代词用that（不用which）的情况：
1. 先行词是all, anything, everything, nothing等,关系代词应用that
That's all that he told me.
2.先行词前有the only, the same, the very 或no, little, much, any, every, all 等修饰时,关系代词应用that
She is the only person that I know in this company.
3. 先行词前有序数词或形容词*修饰时,关系代词常用that
The first thing that I want to do is to take it away.
4. 当先行词同时含有"人"或"物"时,关系代词应用that
5. 在固定结构the same...that...; so...that...; such...that...以及it is/was...that...的强调句型中,要用that
This is the same park that we once visited.
6. 如主句以there be开头时,关系代词应用that
There is a room that has two windows.

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