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Dear Jadhav Ranjeet,
Good day! Thank you for sharing your experience in our community.
Per your description, you want to provide additional authentication for those users and groups while accessing those folders which they have permission in SharePoint Online.
Based on my experience, currently there is no out of box way to provide the additional authentication method. We can now only provide unique permissions to users. Given this situation, we recommend that you submit requirement for this feature in the feedback portal: Multi-factor authentication for individual sites · Community (microsoft.com), Add multi-factor authentication function · Community (microsoft.com), and many members who has the same requirement with you will vote it in the future. The higher votes, the more attention the related team will pay on. Many good ideas have been taken in this way. Your voice is also important to us.
Appreciate your understanding.
Sincerely,
Jazlyn | Microsoft Community Moderator