Google Analytics is more accurate than Google Webmaster. Google Analytics Measures users interactivity on a website. Google Webmaster mostly describe website structure, keyword relevancy and a brief idea about keywords.

Google Search Console uses Clicks which will count every time a person clicks on your results in the SERPs, regardless of whether it is the same person or if there are multiple clicks in a short period of time.

In your Google Analytics custom report, you are using Users, a calculated GA metric based on a single identifier (Client ID or User ID).

How can we explain the differences in your reports?

1. If a person performs several Google searches and clicks three times on your results within 30 minutes, GSC will show 3 clicks but GA will show only 1 user. You should use Sessions instead of Users in your custom report.
2. If a person clicks twice on your results in the SERPs within 30 minutes, Google Analytics will only record as a Landing page the first URL that was visited (essentially the arrival point during that session). Using Landing page as a dimension in your custom report will exclude actual organic traffic. In this case, there is no quick fix to get the data, since if you use Page instead of Landing Page you will get the organic sessions that went through those URLs but not just the ones that were arrival point.

In summary, you are not using the correct metric/dimension in Google Analytics to get the data you are looking for. In the following image, assuming that all page views are organic and first access (landing page), the results would be:

• GSC: 9 clicks
• GA: 1 user, 3 sessions, 3 landing pages, 9 pageviews