The good news is, it’s not just you! When Google Search Console was updated from Google Webmaster Tools they changed a few key concepts which we will go over.
In the good old days of Google Webmaster Tools, impressions were counted for each search result you had on the page, regardless of how many results went to the same property. Now, Google Search Console merges impressions.
Here is an example of impressions and other metrics being pulled from search console:
Now here is a snapshot from Google Analytics:
You will notice a small difference, across all of the metrics. This shift will be exacerbated if your website shows up twice on the same search result page frequently.
To fix the metrics so that they match across platforms, webmasters can apply a dummy filter (like a page filter) to break the impression merging.
Then the metrics will line up like below:
You will also note: in Google Analytics SEO reports, your query data is not just limited to the “top 1000 keywords by click” report that shows up on the Search Console Reports. This is important for factoring your long tail keywords into your high-level groups.
The Search Console automatically narrows down to the typical Google Search (Web), whereas Google Analytics’ Search Console integration combines image and video searches.
Understanding this information can help you and your stakeholders comprehend and trust the results you see across these platforms. It is important to realize the strengths and weaknesses of these platforms and seeing how the Google Analytics integration for Search Console provides different value than the Search Console UI.
To find a complete list of comparisons you can reference this supporting article.