"If I don't use my brain, I will lose it" uses the correct construction. It should be noted that I don't find the idea of "losing your brain" to be very natural but I can understand what you're trying to convey. I would probably say something like "If I don't use my knowledge, I will lose/forget it". But, for now, let's stick with the words you've used. Here are the possibilities:
If I don't use my brain, I will lose it.
If I didn't use my brain, I would lose it.
If I hadn't used my brain, I would have lost it.
If you're talking about a general state of affairs, you could say "If you don't use your brain, you lose it".
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