Songfacts®:

• Lead singer-guitarist Patterson Hood wrote this Country Gothic ballad about his first cousin once removed, who died at the age of four, before Patterson was born. The death of Bonnie, while central to the song, is not the focus of the story; rather, Patterson portrays the family's emotions and the fact that Bonnie's everlasting presence remains with the family decades after she is gone.
• Bonnie is described as a "swollen angel", suggesting she might have had a kidney disease. Bonnie's father, Patterson's great-uncle, was an extremely religious man, who believed that Bonnie's illness and death were intended by God as a punishment, not of her, but of himself.
• In interviews, Patterson reveals that he grew up hearing the story of Bonnie's life and death, and that it had a profound effect on him. Singer-guitarist Mike Cooley adds that one good thing about Bible Belt mentality is that it allows you to express yourself without judging the people you're describing. >>

  Suggestion credit:
  Ekristheh - Halath, for all above