Because of the strain that using the dōjutsu puts on his eyes.
Usually, all dojutsu strain the eyes to some degree. However, Amaterasu is unique in that the stress it puts on the eyes is consistant even after Sasuke received an Eternal Mangekyo Sharingan. Even after the transplant, Sasuke’s left eye continued to bleed to some degree whenever he used Amaterasu. Even his eye evolving into a Rinnegan didn’t change this.all normal Mangekyo Sharingan users get progressively more and more blind the more they use their Mangekyo Sharingan. By the time Itachi was fighting Sasuke, he vision was so blurry he could barely see straight.
Amaterasu causes the eye to bleed regardless of the form, however, the bleeding isn’t really attributed to the blindness, as you can use Amaterasu and bleed from the eye with the EMS like Sasuke, and no long-term damage will come to your eye.