In SharePoint 2013, which one is best practise to configure Reporting Services in
SharePoint Integration mode or
Based on which consideration we can choose? Which mode is best and what are the difference between the two?
I'm assuming that you're using SharePoint already...
The two modes are:
In SharePoint integrated mode, reports are stored in SharePoint, and if that's the place that people within the organisation go for information, then SharePoint is a logical place to store these reports and for users to access these reports. If you're using native mode, then the user has to be directed to the Reporting Services instance to view their reports. It's worth noting that there's a performance hit running Reporting Services in SharePoint integrated mode.
Check out the additional features that are supported by running Reporting Services in SharePoint integrated mode at https://msdn.microsoft.com/en-us/library/bb326290