It is lève-toi when positive, but ne te lève pas when negative.
Why does the pronoun itself and its position change? Is this an inconsistency? What does native speakers think about it?
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The "irregular" form is the positive imperative which uses the stressed pronoun toi after the verb.
All other French tenses use the unstressed reflexive pronoun te:
Tu te lèves
Tu ne te lèves pas
Tu t'es levé
Ne te lève pas !
It's a pattern among romance languages imperatives:
Spanish: ¡Levantate! / ¡No te levanta!
Italian: Alzati! / * Non ti alzare! (but also Non alzarti)
Catalan: Aixeca't! / No t’aixequis!
Romanian: Ridică-te! / Nu te ridica!
In spoken French, ne is often dropped leading to:
Te lève pas !
A more radical evolution builds the negative imperative from the positive :
Lève-toi pas !
This last form is probably not in your French grammar book, though.