In Magento, if you want to change canonical URL for just one category or quite a few categories, and don’t want to affect rest of the canonical URLs then do the following.

Note that this is helpful when you already have canonical URL in the page and want to REPLACE it with new url. If you don’t have canonical URL at all then you might want to ignore the first action tag in the below code.

– Go to the category page you want to change canonical URL in Magento Admin
– Click the tab “Custom Design”
– In the Custom Layout Update textbox, paste this:

<reference name="head">  
 <action block="head" method="removeItem">  
 <item>link_rel</item>  
 <name>http://loca.lho.st/old-canonical-url</name>  
 </action>  
 <action method="addLinkRel" translate="title">  
 <rel>canonical</rel>  
 <href>http://loca.lho.st/new-canonical-url</href> </action>  
</reference>

Change http://loca.lho.st/old-canonical-url and http://loca.lho.st/new-canonical-url with your desired URLs and save the category.

Basically first action tag in the code removes old canonical URL and second action tag adds the canonical URL with the new value you specify.

You may also need to clear cache.

HTH!