Hmm, not sure what's causing the confusion here. You did translate the phrase, didn't you? Your brain is basically all that you are, so it makes sense to take care of it. Don't know, maybe it's your translation that's somehow ambigous to you.

Let no harm come to your head, it contains your brain.

Anyway, this phrase is somewhat of a joke. For example you can say that to someone who wants to go out when it's freezing without a knit cap on their head. On a sidenote, let's see how you can crack a similar one.

Не ковыряй в носу, мозги поцарапаешь!

UPD

I also found this
click

I suppose you actualy heard and saw this one. It's a bit funnier like this and with wider "application"