Canonical tags tell search engines the URL for the original content of a page. A popular and effective use of canonical tags is to set them on every page to make it clear which version is the primary one. For example, is it https://yoursite.com/page or is it http://www.yoursite.com/page/? Things like www, https or trailing / can all be seen as different versions, so it’s important for SEO purposes to tell search engines which version is the right version. Given that your website’s URL is properly defined in your _config.yml file, just insert the following in your header/head layout:
<link rel="canonical" href="{{ site.url }}{{ page.url | replace:'index.html',''}}">
As you can see, it’s fairly easy to insert a canonical tag for every page of your Jekyll website by using some simple liquid syntax. The | replace:‘index.html’,‘’ part just ensures that your homepage doesn’t come up as index.html.
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I have also research Update on Canonical Link Tag: Currently, Jekyll-SEO-tag merges site URL with page URL and generates the final canonical URL. If for a specific page canonical_url is explicitly defined by the user, we can assign the URL to the canonical URL otherwise use default generated URL.
Here is my implementation: