Don't keep it charging is perfectly comprehensible, but it's not exactly how I'd say this.
Don't keep it plugged in overnight, that wastes energy.
This has the same meaning as charging, but I think it's a more common way to say it.
Also note that I changed the comment to say you're wasting energy; the way you've written it it's implied that keeping it charging overnight is what does save energy:
Don't (keep it charging overnight [in order] to save energy)
Obviously that's not what you mean, and everyone would know that, but semantically what you're saying there is "Charging it overnight saves energy. I don't think you should save energy, so don't do that."
If you wanted to use charge, you can, I just wouldn't pair it with keep:
Don't charge your phone overnight; that wastes energy.
(The semicolon here has the same function of clearing up the ambiguity.)
If you want to use saves energy, you could say something like these:
If you don't charge your phone overnight, you'll save energy.
You'll save energy if you don't charge your phone overnight.