It's an autobiographical song telling us about how Christina felt after she decided to stop running back to a guy who continued to cheat on her.
She dated a guy who cheated on her. They'd break up, then he'd come back and they'd get back together. This became a cycle.
One day, while they were broken up, she was visiting family at home. She was hiding in her bedroom because she heard that he was looking for her again. She said she really wanted to go see him, but couldn't handle going through that one more time, so she wrote "Jar of Hearts" instead.