Just started a fresh project, unity version 2021.3.0fl. Beside Naninovel, the only thing I've done is updated the unity ads. When i press play, there are 2 event systems in the scene. Please ensure there is always exactly one event system in the scene
UnityEngine.EventSystems.EventSystem:Update () (at Library/PackageCache/com.unity.ugui@1.0.0/Runtime/EventSystem/EventSystem.cs:514)

It's coming from Unity UI automatically, and I don't know how to stop it so Naninovel can get priority. Any help?

You can prevent Naninovel from spawning an Event System in the Input Configuration.
https://naninovel.com/guide/input-proce ... processing