“Clean as a whistle” usually means very clean. If a room, dish, car, or shirt is described this way, the speaker means it is spotless or neatly cleaned.
The expression can also mean clear, smooth, or pure, especially in older or broader use. That second sense helps explain the likely origin. A whistle produces a sharp, pure sound, so the phrase probably developed from the idea of something being clear and free from roughness or dirt.
Some people assume the phrase refers to the shape or polished surface of a whistle, but the clearer link is probably the sound. In English, clean has long been used for things that are pure, exact, or unobstructed, not only physically tidy.
- The kitchen was clean as a whistle after the party.
- His final note was clean as a whistle.
So in modern English, the most common meaning is simply very clean. In some contexts, especially with sound or movement, it can still suggest something clear and smooth.