Dr. Jekyll realizes that the human body is more malleable than most people recognize, more like a "mist." He therefore concocts a potion that can rearrange his body so that, as he puts it, the "lower elements" of his "soul" can become dominant.

After he drinks this potion, he feels pain, nausea, and a "horror of the spirit." He alludes to this as birth "agonies." When he recovers, he feels like he has gotten over an illness.

At this point, he begins to feel elated. He feels lighter, younger, and more physically "happy," and he feels sensuality running through him. He experiences recklessness, knows he is now far more capable of evil than he was, and yet he is excited by the prospect. He feels freed from former "bonds of obligation"—in other words, freed from conscience and superego.

He also quickly realizes he is smaller. He has shrunken, he surmises, because the evil him is less developed than the good.

The transformation shows both his awareness that he has become evil as Mr. Hyde and the seductive allure of this change.

Physically, he feels very bad as the transformation is actually taking place.  It hurts him very terribly.  He says that he feels the "most racking pains."  He says that he feels like throwing up.  All in all, it sounds like it is very unpleasant.

But then after he has become Mr. Hyde, he actually feels pretty good.  He feels like he is much younger than he had been.  He feels like he is lighter as well.  He has all sorts of exciting thoughts running through him.  He feels free, but it is not an innocent kind of freedom.

So it hurts to get that way, but he actually feels pretty good as Hyde.