iOS 64-bit support is implemented with the scripting backend called IL2CPP. It runs with your C#/UnityScript code.
The IL2CPP runtime combines an ahead of time compiler with a virtual machine to convert assemblies to C++ while leveraging standard platform C++ compilers to produce native binaries. The net result is significantly higher performance, platform compatibility and maintainability.
IL2CPP is the only scripting backend to support deploying to ARM 64-bit on iOS, and is thus mandatory to deploy to the Apple App Sstore for releasing new apps.
To read more about IL2CPP, see the blog posts The future of scripting in Unity and Apple iOS 64-bit support in Unity.
Select IL2CPP in the Scripting Backend drop-down menu in Player Settings.
By default it will build for Universal architecture (including both ARM64 and ARMv7); if needed you can switch to specific architecture in Player Settings. There are a number of things that should be done before your application is up and running in 64-bits:
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