Eating behavior problems significantly affect the physical health and quality of life of children with autism spectrum disorder and intellectual disabilities (co-occurring ASD/ID). This study aimed to evaluate the effects of a 12-week Ball Combination Training Program (BCTP), continuous theta burst stimulation (cTBS), and an intervention combining both (in the CIG) on the eating behaviors of children with co-occurring ASD/ID. A total of 48 participants were assigned into one of four groups: the BCTP ( = 13), cTBS ( = 12), the CIG ( = 11), and a control group ( = 12). The intervention groups received their respective treatments in addition to the routine institutional rehabilitation, whereas the control group only received the standard institutional rehabilitation. The intervention outcomes were assessed using the parent-reported Children's Eating Behavior Questionnaire (CEBQ). The results indicated that all three intervention methods led to improvements in their eating behavior after 12 weeks. Specifically, the BCTP group and the CIG demonstrated significantly reduced Food Fussiness behavior, while the children's Enjoyment of Food was markedly enhanced in the cTBS group and the CIG. Furthermore, the CIG experienced a particularly notable effect in terms of the improvement in the Satiety Responsiveness dimension of their eating behavior. Among the three approaches, the CIG demonstrated a clear advantage over the single interventions in terms of both the breadth and magnitude of its improvements. This study confirmed the effectiveness of these three intervention strategies in addressing dietary behavior problems among children with co-occurring ASD/ID. Future research should focus on exploring the combined intervention approach further, particularly its potential synergy, while delving deeper into the neural mechanisms underlying these behavioral improvements.