I want to remove user to access reports form classic. But the same user should access reports from lightning. Do any one have any idea how to handle this?
Unfortunately, there is no way to remove classic access to the Reports. If you remove system permissions to access reports and dashboards in classic, users won’t be able to access reports and dashboards in LEX too. As suggested in the comments, the only alternative would be to remove the "switch to Classic" experience.
Recommend you to checkout LEX adoption strategies
You can remove the Embedded classic report builder by Hiding the embedded Salesforce Classic report builder in Lightning Experience to have better adoption to LEX Reports. With this, users no longer see the New Report (Salesforce Classic) and Edit (Salesforce Classic) buttons on the Reports tab in Lightning Experience.