Google will rank sites lower should they serve intrusive pop up ads.
In planned changes to how it ranks sites the search giant said ti iwll change its ranking on January 10th 2017.
In a blog post it said:

Here are some examples of techniques that make content less accessible to a user:

Showing a popup that covers the main content, either immediately after the user navigates to a page from the search results, or while they are looking through the page.

Displaying a standalone interstitial that the user has to dismiss before accessing the main content.

Using a layout where the above-the-fold portion of the page appears similar to a standalone interstitial, but the original content has been inlined underneath the fold.Read the blog.