- MasterUrl is used to change the layout of all end user pages while CustomMasterUrl is used for changing the layout of admin pages.

MasterUrl: This master page will be used for system pages (ghosted) like list / library forms, site settings, view all contents pages.CustomMasterUrl: This master page will be used for all publishing pages in pages library or site pages library.

MasterUrl is the property which is used to set master pages for all forms and non publishing pagesCustomMasterUrl is the property used to set the master pages for publishing sites.