At the start of the story, Lizabeth is very immature, and enjoys harassing Miss Lottie with her friends. They chop off the tops of the marigolds, and mock Miss Lottie. Lizabeth has no compassion when it comes to the emotions and wants of others, particularly Miss Lottie, whom Lizabeth sees as strange and different, and it's never crossed her mind to respect Miss Lottie.
As the story progresses, Lizabeth notices strange feelings of guilt for what she does with her friends. She also overhears her parents arguing about having nothing. She begins to realize the misfortune of herself ad others, and her journey towards realizing compassion begins. She can't stop thinking about how mean her and her friends are to Miss Lottie.
Father (In Distance): "Twenty-two years, Maybelle, twenty-two years, and I got nothing for you, nothing, nothing...."
Finally, at the conclusion of the story, a confused, emotion-filled Lizabeth decides to strike out at the fact that her childhood is fading, and that she's growing up and maturing faster than she'd like by destroying Miss Lottie's marigolds in a childlike fit. After the destruction is over, she realizes what she's done, and as she looks into Miss Lottie's eyes, she can see a unique, emotional, different person than herself for the first time. This lesson in compassion, that she now understands, and has for Miss Lottie, is represented through the destruction of the marigolds, symbolizing Lizabeth's loss of innocence.