In Act 2, Scene 1, Sebastian first relays to Antonio that Viola is his twin sister, born within the same hour as he, and he wishes they had both died together in the same hour. His grief over her loss is very profound indeed. However, he also describes his sister to Antonio. One thing he says is that even though they looked alike, many thought she was beautiful. He apparently feels it hard to see his sister as beautiful when he sees that she looks so much like his own masculine self, which we see him stating in his lines:
[T]hough it was said she much resembled me, was yet of many accounted beautiful: but, though I could not with such estimable wonder overfar believe that. (II.i.21-23)
However, he also tells Antonio that regardless of not being able to see her as completely beautiful, he certainly did see her mind as being beautiful, even enviable. Hence from these speeches, we learn that Sebastian cared very deeply about his sister and highly valued her mind, meaning her intellect and character.