The story of Wonderful Life follows the exploits of Han Seung Wan. During a trip to Singapore to meet his girlfriend, Lee Chae Young, he bumps into a young woman named Jung Se Jin  at the airport. They accidentally swap their passports, which leads Se Jin to track Seung Wan down at the address pasted in his passport. She meets a man, Min Do Yun, who kindly gives her a piggyback ride to the apartment. When they meet again in Chae Young's apartment, they exchange passports, on the condition that Se Jin helps Seung Wan track down his missing girlfriend. They discover Chae Young playing around with Do Yun, the two of them having met in Australia, much to Seung Wan's surprise. Depressed that his girlfriend is now spending time with Do Yun, Seung Wan turns to Se Jin for comfort. The duo drink too much, resulting in a one-night stand in the Sentosa hotel.

Being a devout Catholic, Se Jin asks Seung Wan to take responsibility for his deed. The immature Seung Wan leaves her, both returning home to Korea at an earlier date than scheduled. They move on with their lives until Seung Wan is thrown out by his father for spending too much money on liquor. With nowhere else to go, he contacts Se Jin for help.

Se Jin agrees to help him earn money to pay back his father, but is shocked after being introduced to his brother and sister-in-law at her job (she works in an amusement park-like restaurant, where she agreed to let Seung Wan work as well), who lead her to realize that her increased appetite and vomiting as of late are symptoms of pregnancy. Disguising herself in a red wig and skin-tight dress, Se Jin visits the pharmacist to buy a pregnancy test kit, only to run into Do Yun. While trying to escape, she twists her ankle, and Do Yung again gives her a piggyback ride home. Se Jin leave Korea for studying abroad in Australia.

A year later, Se Jin's nosy sister presents the baby, Shin Bi (Jung Da-bin), to her biological father. Seung Wan and Se Jin decide to get married for the baby's sake, but draw up a list of rules that they must abide by, including the possibility of divorce in five years time. Although the couple suffers extreme financial difficulties, Seung Wan takes a job in his father's construction business to support the family, but is forced to leave for military service shortly thereafter.

Upon his return, the reunited Seung Wan and Se Jin face new challenges. While the former juggles chores due to his continuing studies to be a pilot, the latter struggles to find employment in a job market that discriminates against her for being a mother. Ultimately, however, Chae Young gets her an interview at the Kidsbear company where she works, though her assistance hides jealous intentions; aware of Do Yun's feelings for Se Jin, Chae Young plots to regain her former boyfriend by breaking up the family. Se Jin is hired by Kidsbear despite verbal attacks on the department store's CEOs, but she and her husband must deal with constant relationship problems brought on by Chae Young's interference.

While much of the series is consumed by the interactions of the four principal characters, the final stretch of Wonderful Life proposes an ultimate test to Seung Wan and Se Jin's roles as parents and judges whether or not the decisions they made in the past were truly correct, questioning the morality of their actions. Shin Bi is diagnosed with leukemia, and her parents are cursed to hardship in searching for a viable bone marrow donor.