Early short-term intensive insulin (STII) therapy can induce drug-free glycemic remission for up to 1 year in half of newly diagnosed type 2 diabetic mellitus (T2DM) patients. Whether exenatide following STII therapy will induce higher long-term glycaemic remission is currently unknown. To assess the effect of STII+ exenatide therapy, compared with STII only, on maintenance of glycaemic remission in newly diagnosed T2DM patients. In this randomized, parallel-group, open-label, controlled trial, 129 patients (66 in STII+ exenatide group and 63 in STII only group) firstly completed 3-week STII therapy, then STII+ exenatide group was treated with exenatide for 12 weeks further. The cumulative probabilities of 1-year and 2-year glycaemic remission in STII+ exenatide group were 68.2 ± 5.7% and 53.0 ± 6.1%, which were significantly higher than STII only group (36.5 ± 6.1% and 31.8 ± 5.9%) (p-values < 0.001). Patients in STII+ exenatide group, compared with STII only group, showed significantly decreased levels of waist (82.2 (81.0, 83.5) cm v.s. 84.2 (82.7, 85.7) cm, p = 0.048) and HbA1c (5.83 (5.60, 6.06)% v.s. 6.49 (6.20, 6.77)%, p < 0.001) after 12-week exenatide treatment, but these differences disappeared after 1-year and 2-year follow-up. As conclusions, Improved effect of sequential exenatide after STII therapy on maintenance of glycaemic remission only occurred during exenatide treatment and lost upon treatment cessation.