There are different ways to deliver your Flutter app into Apple App Store, I will show you the easiest way to do so using Apple's application called Transporter. After you have set your app in the Xcode with all the configuration, follow these steps
Change app version in ios/Runner/Runner/xcodeproj/project.pbxproj
flutter clean
Run the following command in you terminal
flutter build ipa
After building the Flutter app and installing Transporter, Drag and drop the built ipa inside the /build/ios/ipa
into Transporter.
Press on the 3 dots next to deliver and press verify. If there are errors in your delivery, it will be shown, and you have to fix them and then repeat the previous steps.
After verifying without errors, click Deliver