@Richa Kumari , In General, VPP can deploy both free and paid apps. But iOS store app is only for free app. If you want to deploy free app, both are OK. The difference I can find is that the iOS store app is only an approved App that the user has to receive using his own Apple ID. iOS VPP apps are already bought by your organization and can be installed on devices even without Apple IDs. VPP is a licensing and deployment model specific to iOS and really has very little to do with Intune or how an app works on a device. Here are some articles for your reference:
VPP iOS apps
https://learn.microsoft.com/en-us/mem/intune/apps/vpp-apps-ios
iOS store app
https://learn.microsoft.com/en-us/mem/intune/apps/store-apps-ios
Hope it can help.
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