I think its basically because she's self-centered and narcissistic. It's mentioned that she didn't like how he looked like his dad . She hated her husband, and her youngest looked like him. Her oldest did look like her so that was her person. She was losing her career and basically needed to blame someone for all her issues and her mini me's issues so the son that looked like her husband was a good choice to blame.

Why would the mother hate her own biological son??? THEY ARE BOTH HER SONS! It doesn't make sense for them to hide the older brother and have Hajin (mc) the only heir. Also why would they switch the brother's background like this whole mess could have been avoided. Also why did the father mellow out? Was he not abusive in the beginning??? Where is the real yoo hajin in the novel? How did mc come to posses the novel hajin? (The novel hajin and shin kim should get together as some sort of redemption arc/spin off bc I do pity them) He never cleared it up w seonwoo that he's a transmigrator??? why did there need to be a time skip seperation he couldve just studied w seonwoo to get admission? idk man i really like the concept but the execution of the plot was lack luster. The only sensible explanation to me would have been if they dad had an affair w another woman and Hajin was their love child and since the dad favors the mistress they swapped the identity of the siblings.