The most popular theory for why Sophie chose to save her son over her daughter is that she may have thought that her son would have a better chance of surviving the concentration camp than her daughter would have had. He was older and boys were considered to be stronger and more resilient than girls.
Sophie had to quickly choose one of the children to die, or they would both be killed. She likely didn't have time to think about the choice, so she had to pick one or the other. Her choice haunted her for the rest of her life because there was no good choice. How can a mother choose between either of her children?