Two places to check:
- Set the resoltion in Unity, in the Player Settings (in your projects settings, or accessible on the Build settings page)
- Set the resolution of the player on Itch. When you select that the file will be played in the browser, you will see a bit below that there will be an option to set the resolution of the player. Just make sure it matches what you put in the player settings!
Also, if both of these do not work, look at your UI canvases in your Unity project to ensure elements have the correct anchors and pivot points. For WebGL, I prefer to set my Canvas scaler to scale with screen size and put everything in the same resolution I will end up using in itch.