To have a very angry expression; to be full of rage or hostility

I don't know what happened to him but I didn't dare ask because he had a face like thunder and he was obviously mad as hell

Non so che cosa gli sia successo, ma era talmente nero che non ho osato chiederglielo

Seeing her precious flower beds being completely messed up by the neighbor's puppy, Marianne stood there with hands on her hips, staring at the little culprit with a face like thunder

Vedendo le sue preziose aiuole completamente distrutte dal cucciolo dei vicini, Marianna se ne stava lì, con le mani sui fianchi, cupa in volto, a fissare il piccolo colpevole

It's clearly a comparison to the black clouds that accompany a thunderstorm