1. I think you are not serious, are you?

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Does 'serious' mean 'injured severely'?

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2. I don't think he is serious, is he?
(Does 'serious' mean 'thoughtful' or 'injured badly' here?)

http://www.dictionary.com/browse/serious?s=t

In these questions, the word means "thoughtful" and has nothing to do with being injured.

If you say, "He had serious injuries," you mean his injuries were severe, but usually "serious" means what's given in the linked dictionary entry above.