On the bus I saw a student ( ) I thought was your brother.

WHO 可以做主语，又可以做宾语
WHOM只能做宾语

你这道题里，student是was your brother的主语，应该从这方面想
而不是从I though 的宾语这方面想

[解题过程]
who和whom在定语从句中作关系代词时：
1.who指人，在从句中做主语
(1) The boys who are playing football are from Class One.
(2) Yesterday I helped an old man who lost his way.
2. whom指人，在定语从句中充当宾语，常可省略。
(1) Mr. Liu is the person (whom) you talked about on the bus.
(2) Mr. Ling is just the boy whom I want to see.

同意楼上意见，I thought 在这里是插入语，考究语法就要忽略不计，句子自然变成On the bus I saw a student ( )was your brother，在对于student的定语从句()was your brother.中需要一个主语，当然只能用who做人的主格形式来充当主语了。楼上将英语学活了，见多识广啊。

句子中的I thought 是插入语，句子的主干应该是On the bus I saw a student ( )was your brother，根据定语从句的知识，很容易知道应该填who