Is your homepage not appearing after you do a site: search? Or your homepage is simply not ranking for its keywords?
Your site is being penalized. Here on bhw is more than enough topics how to solve it.
This. Op check your incoming links anchor profile to your homepage. If they are high adjust.
Is your site an EMD?
How long has it been gone? It usually disappears for a while once you start building links, and indeed as you add more. Though, assuming it's not penalized, it will bounce back stronger than before.
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It is keyword rankings for my inner pages keywords.
but my main keywords not even in 1000
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You don't have the keywords in your homepage, I'm guessing its blog type and you update your content from time to time. You have articles who are ranking to specific keywords, you really don't need to worry about your homage nor ranking