If you’re talking about the main interface colours for the binder background, the editor, etc., these are common to all projects. You can save the appearance preference settings as a theme, however, from the “Manage…” menu in Scrivener > Preferences, and you can then quickly switch between themes when you change projects.
Label and keyword colours are project-specific, but if you have a set of colours you typically like to use for certain types of projects, you could set up a project with those labels and keywords, then use File > Save As Template… to create a new base template for future projects of that type which you can use instead of the built-in default.