If my height is more than my brother I say:
I am taller then my brother
but if my height is less, which sentence is correct?
I am smaller then my brother
I am shorten then my brother
I am lower then my brother
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First of all, I would point you to Better then vs better than, as you should use than, not then.
As to your actual question:
I would say
I am shorter than my brother.
You could also say
I'm not as tall as my brother.
However, I would only use the second one in response to someone saying something like
You're so tall!
Otherwise, it would sound odd to me, though it's still grammatically correct.