I'm assisting a customer upgrading their existing legacy Exchange 2010 server. However, I found the version number I got from the Exchange Management Shell is different from the Exchange Management Console.

The service is running at the moment and the email is functioning.

Is that safe to ignore? Which is the real version installed?

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The version number you can see from Get-ExchangeServer only displays the latest Service Pack; in order to check the actual installed Update Rollup, you need to go to the Control Panel. Also, the version number you can see from the EMC isn't relevant at all.

Here are the current version numbers for all Exchange 2010 SP3 rollups: https://social.technet.microsoft.com/wiki/contents/articles/240.exchange-server-and-update-rollup-build-numbers.aspx#H

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    Ok, I went to control panel -> programs and features. The version number is showing, just as same as the one I saw from the management shell. However, if I list the installed updates, I could see the rollup was installed there. Thank you. – NeilWang Jun 20 at 20:51

Agree with Massimo, you could view the current service pack version via the cmdlet Get-ExchangeServer, and view the installed Rollup version via EMC or Control Panel.

Besides, the following command can also tell you the current RU version and SP version:

Get-Command Exsetup.exe | ForEach-Object {$_.FileVersionInfo}

And the following related blog is for your reference: How To Check Exchange Rollup Version

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