Thomas' mother appeared in many of Thomas's memory-dreams. She seemed to love her son very much.
In The Scorch Trials, Thomas had a memory-dream of her crying as she told young Thomas, "I don't understand why they chose you." Presumably, she was referring to WICKED having discovered that he was Immune and choosing him for the Trials.
Eventually, she contracted the Flare herself, presumably going mad before dying.
Her appearance is not really described in Thomas' flashbacks. She appeared to be young, perhaps in her thirties, and light-skinned.