@Jian Wu, Thanks for posting in Q&A.
From your description, I know you want to stop a specific iOS App from auto update while allow others via Intune.
Based on my research, if the apps were deployed from iOS app store, the store itself controls the apps and their updates and there is no way to control apps auto-update.
https://learn.microsoft.com/en-us/mem/intune/apps/apps-add#app-types-in-microsoft-intune
If the apps were VPP and deploy via Intune, for one specific app, you can configure Prevent automatic app updates to Yes under Assignment session to prevent it auto-update, which is set by default No, also the assignment type must be required.
Non-official, just for reference.
Hope above information can help you.
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