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Introduction Dietary intervention is fundamental for the management of type 2 diabetes (T2D), playing a crucial role in stabilising blood glucose levels and improving quality of life. As the major contributor to daily energy intake, the quality of carbohydrates can directly influence the glycaemic stability. Therefore, we aim to explore whether adjusting and optimising the composition of dietary carbohydrates, specifically starch, can provide multiple metabolic benefits for patients with T2D.Methods and analysis This multicentre randomised crossover clinical trial will include 150 participants with T2D. Participants will be assigned to either a conventional diet (CD) following the guidelines for T2D or an optimised carbohydrate diet (OCD) focused on increasing resistant starch intake to 40 g/day and decreasing rapidly digestible starch intake for 12 weeks. This will be followed by a 6-week wash-out period, after which participants will crossover to the alternate diet with equal energy and consistent energy proportion of the three macronutrients for another 12 weeks. The primary outcome is the difference in the change of postprandial glycaemia (changes in the average incremental area under the blood glucose curve (iAUC)) induced by OCD and CD interventions. Secondary outcomes include changes in other glucose and lipid metabolism-related parameters and cognitive function, as well as psychological, behavioural and physiological factors. Exploratory outcomes include changes in the iAUCs for each of the three meals, appetite-related hormone levels, degree of hepatic steatosis, serum cytokines, immune functions and multiomics parameters.Ethics and dissemination The protocol has received approval from the Ethics Committee of Shanghai Sixth People’s Hospital (Approval No. 2025–018; Protocol V.4.1, 20250112) and has been registered with the ClinicalTrials.gov Registry. The findings will be disseminated through peer-reviewed journal publications, conference presentations and media releases.Trial registration number NCT06936657.