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I read https://japanese.stackexchange.com/a/25378/45347, which says in Japanese, main clause's tense is relative to now, and subordinate clause's tense is relative to main clause's tense.

But I can't understand these two sentences, if the former means "I thought なおみ was in the school", what does the later sentence mean?

私はなおみが学校にいると思った。
私はなおみが学校にいたと思った。

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  • That answer clearly explains the difference: "The former implies that the speaker thinks Naomi is at school as he's thinking, while the latter means the speaker thinks Naomi was at school sometime even further in the past (but probably somewhere else at the time of thinking)." For example, 私 thought yesterday that Naomi was at school when some incident happened one month ago.
    – naruto
    Commented May 1, 2023 at 5:02

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I don't know how rigid tense concord really is, but according to (my understanding of) the standard teaching English grammar in Japan, 私はなおみが学校にいたと思った should be translated as I thought that Naomi had been at school. Since いた is inside the clause, its past tense refers to the past with respect to 思った, which is already past, so that いた is actually pluperfect1.

On the other hand, いる in 私はなおみが学校にいると思った refers to the same tense as 思った, so it is rendered as was (at school).

1 I'm not sure it is the right terminology.

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