Few studies have been conducted to evaluate the effect of xylitol on the virulence and morphology of Streptococcus mutans (S. mutans). This study was conducted to evaluate changes in the morphology and virulence of S. mutans in response to long-term consumption of gum containing xylitol. Participants were voluntarily recruited for a women's oral health prevention program, classified into two groups (a control and a xylitol group), and then followed for 1 year. Ten salivary samples were randomly selected from each group. Colony count, field emission scanning electron microscopy, and real-time reverse transcription polymerase chain reaction were used to analyze the characteristics of S. mutans. In the xylitol group, the colony counts of S. mutans decreased steadily over time. In addition, the adherence of the colonies in the xylitol group became weak, and the size of the colonies decreased compared to the control. The secretion of sticky substances from the surface of S. mutans colonies and gtfB gene expression also decreased in the xylitol group. These findings indicate that regular chewing of xylitol gum over a long period may lead to decreased gtfB expression, which can negatively affect the synthesis of extracellular polysaccharides by S. mutans, which could reduce the size and growth of S. mutans colonies and change their morphology as a result.