Humans are widely exposed to environmental chemicals, yet evidence integrating multiple behaviors and environmental factors remains limited, particularly among generally healthy adolescents. We examined the associations of lifestyle behaviors and residential environmental factors with urinary concentrations of phthalates (PEs), organophosphate flame retardants (PFRs), and bisphenols (BPs) among 420 Japanese early adolescents aged 9-12 years. Parents completed a questionnaire on plastic kitchenware use and heating frequency, personal care product use, fragranced product use, and residential environmental factors. Urinary chemicals were quantified using LC-MS/MS or GC-MS/MS. Associations were assessed using multivariable regression analyses, and machine learning models were used to evaluate the relative importance of contributing factors. Although overall chemical exposure levels were lower than those reported worldwide, several potentially changeable lifestyle behaviors and residential environmental factors were identified. A higher frequency of heating plastic kitchenware was positively associated with ΣDEHP and BPS levels (p for trend = 0.008, 0.025, respectively). A higher frequency of household fragrance use was positively associated with DnBP and ΣDEHP levels (p for trend = 0.029, 0.033, respectively). Presence of PVC flooring was positively associated with ΣDEHP levels (p = 0.003), whereas soap use was inversely associated with BBzP levels (p for trend = 0.019). Machine learning analyses further identified heating plastic kitchenware as an important contributing factor, with heating more than five times per week associated with higher ΣDEHP exposure. These findings suggest that reducing the habit of heating plastic kitchenware and the use of fragranced products, avoiding PVC flooring, together with promoting handwashing with soap, may help lower chemical exposures in adolescents.