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Introduction Childhood overweight and obesity (OWO) in China, especially in urban areas, has become a significant public health challenge. Recent studies indicate a high prevalence of OWO in both children and adults, exacerbated by urbanisation and economic development. This trend poses a threat to health outcomes, including neurocognitive functioning, socio-emotional development and risk of chronic conditions. Recognising the limitations of high-income country prevention models, the Sino-Canadian Healthy Life Trajectories Initiative (SCHeLTI) was established to evaluate a multifaceted intervention aimed at mitigating childhood OWO and related non-communicable disease risks. This protocol outlines the economic evaluation component of the SCHeLTI trial.Methods and analysis A within-trial economic evaluation and long-term model from both a healthcare/personal social services perspective and a broader societal perspective will be undertaken alongside the SCHeLTI study, comparing the multifaceted intervention to usual care. Costs will include intervention provision, implementation and household expenditures. Outcome measures span child and maternal health-related quality of life, growth indicators, cognitive and behavioural development, nutritional status and metabolic dysfunction indicators. Cost-effectiveness and cost-utility analyses will be performed, with incremental cost-effectiveness ratios calculated for primary outcomes and quality-adjusted life years. A decision-analytical model will also project long-term economic and health impacts. Equity impact analysis will assess the intervention’s effects across socioeconomic strata. Sensitivity analyses, including one-way and probabilistic approaches, will be conducted to ensure robust results.Ethics and dissemination The study has been approved by the Medical Research Ethics Committees of the International Peace Maternity and Child Health Hospital in Shanghai, China (GKLW2017-01) and the CIUSSS de l’Estrie-CHUS in Sherbrooke, Canada (MP-31-2019–2967). Results will be disseminated through academic publications, policy briefs, stakeholder meetings and community engagement to inform early childhood development policy in China and similar settings globally.Trial registration number ChiCTR1800017773.