Will Rebuilding My Site Effect My Adwords?

I have just replaced my old site design with a new one. We have pretty strong PPC campaign with adwords, when google picks up the changes will it put a holt on my adwords till it gets re enabled?

It will effect your landing page score for each adgroup, which will have an effect on your positioning in Google Adwords...either in a positive or negative light. I would review your quality score pre-change and post-change.

Yep, what Veto said. Google uses a similar algorithm to the natural search one to determine quality score for landing pages, so keep this in mind when doing the redesign.