Obesity and iron deficiency are global public health problems. Obesity can cause nutritional disorders, such as iron deficiency. Obesity and iron deficiency during the rapid stages of growth and development in children can cause lasting and irreversible damage to the health of children and even into adulthood. Because the economy and living standards are improving, the incidence of childhood obesity increases yearly, at the same time, the incidence of iron deficiency in obese children is also higher. Obesity is closely related to the occurrence and development of iron deficiency, and the coexistence of the two can produce synergistic effects leading to serious harm, which is an urgent nutritional health problem in clinic. By impairing iron absorption, reducing iron excretion within cells, and by competing with the body for iron with the altered gut flora caused by obesity, obesity can disrupt the normal iron metabolism process and then lead to iron deficiency. The mechanism of obesity-associated iron deficiency is complex and may be related to inflammatory response, intestinal cells, anoxic microenvironment and intestinal flora. Therefore, in this review, we discuss possible mechanisms of obesity-associated iron deficiency to offer new methods and strategies for preventing and treating iron deficiency in obese children.