Globally, the high consumption levels of sugar-sweetened beverages (SSBs) and their effect on health have drawn significant attention. This study aimed to identify the consumption patterns of SSBs among children in rural areas of Guangzhou, China, and explore their association with undernutrition. A total of 1864 children aged 9-17 years old were included in this study. Demographics, lifestyle behaviors, and anthropometric and dietary information were collected. Factor analysis was used to identify patterns of SSBs, while nutritional status was assessed using Body Mass Index (BMI). Latent class analysis was used to establish dietary preference models. Log-binomial regression analysis was used to analyze the association between SSBs consumption patterns and undernutrition. The undernutrition prevalence in children was 14.54-19.94% in boys and 9.07% in girls. Three SSB consumption patterns were identified, including the plant protein pattern, dairy-containing pattern, and coffee pattern. Both medium-high (Q3) and the highest (Q4) scores in the dairy-containing pattern were positively associated with the risk of undernutrition, especially in boys. Furthermore, the highest scores in the plant protein pattern and coffee pattern were positively associated with the risk of undernutrition in children aged 9-10 years old. The dairy-containing pattern was a risk factor for undernutrition in children, especially for boys; the plant protein patterns and coffee patterns were risk factors for undernutrition in children aged 9-10 years old. The findings of the study can provide scientific evidence and policy recommendations for improving children's health conditions.