I have to change master page of upload.aspx page. But when I am going to change master page, Sharepoint reastarts automatically. How can I attach new master page with upload.aspx page?
You should NEVER make ANY changes to the out of the box pages installed by SharePoint.
A better solution would be to create a custom application page which either inherits from the upload page base class or else implements some similar code. You will then have total control over the master page that is used as well.
Your final consideration will be how to get your custom upload button visible, this is where you will need to look at a custom feature which uses a combination of custom actions and hide custom action (if you want to hide the existing upload button.)
There is plenty of information on custom actions out there.
The page interits from Application.master, so modifying the same would affect other web applications also.