Clifford Pyncheon is Hepzibah's brother and Judge Pyncheon's cousin. He's the poor sap who Judge Pyncheon framed for murder 30 years before the events of the novel. There is definitely a before-and-after quality to Clifford. We get to see the "before" in the miniature portrait of Clifford as a young man that Hepzibah carries around with her. His face is sensitive and delicate – the face of a man not made for suffering.
The "after" image of Clifford is not so attractive. Clifford's years in prison have been like suspended animation. When he gets out, he is like a child again. He dreams of childish games and takes a child's pleasure in flowers and soap bubbles. That's the good side of Clifford's post-prison self. But we also see a fair amount of the less-good side: the "coarser expression" (7.28) of a guy who has been in the joint and is finally free. He gulps his food and slurps his coffee. He also can't tolerate his poor, devoted sister Hepzibah because she is so ugly. He turns instead to young, pretty Phoebe.
Clifford's relationship with Phoebe is totally platonic and chaste. He just likes to be around this lovely girl who reminds him of what his life might have been before jail ruined it. Still, it's a sign of a serious flaw in Clifford's character that he literally cannot stand to be taken care of by an ugly woman. Hepzibah loves him and wants what's best for him, but Clifford adores beauty and so cannot look at his old, scrawny, scowling sister.
In fact, the narrator comments that Clifford's beauty-loving nature might have led him into dire moral grey areas if he hadn't gone to prison. He speculates that, if Clifford had been able to live as a free man, his delicate taste might have "eaten out or filed away his affections" (7.48). In other words, Clifford might have become all style and no substance. The narrator concludes that it's a shame Clifford had to spend so much time in prison, but at least there is this "redeeming drop of mercy at the bottom" (7.48), that he didn't become a complete tool as a result of his aesthetic feelings.
To this before-and-after picture we've sketched of Clifford, we should add something else: an after-after image of the man once he is free of his old nightmare. With the sudden death of Judge Pyncheon, Clifford is filled with a sudden enthusiasm and glee. He embraces his freedom with the joy of a much younger and less miserable man. He pulls Hepzibah straight out of the rotting old House of the Seven Gables and onto a train heading away from Salem. He chatters quickly and joyfully about the future of mankind, when we will abandon our cold houses filled with ghosts and live like nomads on trains moving endlessly from place to place.
This crazy-euphoric Clifford can't last. He has suffered too much to sustain this much energy. He and Hepzibah have to get off the train and go back to the dark reality of the House of the Seven Gables. But even if Clifford can't keep up this level of joy, he does get much, much better by the end of the book. While it is too late to fix the great sorrow of his 30 years in prison for no reason, he recovers enough of his old intellectual gifts "partially to light up his character" (21.10). His name has been cleared and he, Hepzibah, and Phoebe are moving to Judge Pyncheon's splendid country house. Clifford is "evidently happy" (21.10), which is more than you can say about a lot of characters, including Judge Pyncheon.
The last chapter of the novel also clears up one remaining mystery about Clifford: did he have access to deep secrets of hidden wealth, as Judge Pyncheon believed? Not at all! As a child, Clifford found the hidden compartment with the ancient, worthless deed to the Pyncheon lands in Maine. Hepzibah speculates that "Clifford probably made a kind of fairy-tale of this discovery "[...] and poor Jaffrey, who took hold of everything as if it were real, thought [Clifford] had found out his uncle's wealth" (21.20). Clifford's light-hearted nature led literal-minded Jaffrey Pyncheon to believe something completely untrue, to the downfall of Clifford and Jaffrey Pyncheon alike.