As far as I known, restarting Windows will mean restarting all the services running on it including SQL Server.
To prevent automatic startup of an instance of SQL Server, you may follow the steps.
On the Start menu, point to All Programs, point to Microsoft SQL Server, point to Configuration Tools, and then click SQL Server Configuration Manager.
In SQL Server Configuration Manager, expand Services, and then click SQL Server.
In the details pane, right-click MSSQLServer, and then click Properties.
In the SQL Server <instancename> Properties dialog box, on the Service tab, in the General box, set the value of Start Mode to Manual.
- Click OK to close the SQL Server <instancename> Properties dialog box, and then close SQL Server Configuration Manager.
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