Background Numerous studies were demonstrated the inverse relationship between all kinds of physical activity (PA) and cardiovascular diseases (CVDs), few of them focus on the new-onset hypertension. Therefore, this study was aimed to determine the impact of long-term PA on the risk of new-onset hypertension in type 2 diabetes mellitus (T2DM) patients with pre-hypertension.Methods A total of 268 T2DM patients with pre-hypertension were recruited between January and December 2015, and followed them up until December 2020. All patients were took PA self-assessment. Demographic, clinical, laboratory, radiologic, treatments, complications, lifestyle and clinical outcomes data were extracted from electronic medical records or collected through a structured interview.Results During 5 year follow-up, the incidence of new-onset hypertension was significantly lower in PA group (15.5% vs 35.4%, p<0.01) when compared to the inactivity group. Logistic regression analysis showed that PA (OR 0.337, 95%CI 0.168 to 0.677, p<0.01), body mass index (BMI) (OR 1.138, 95%CI 1.019 to 1.272, p<0.05) and glycosylated hemoglobin (HbA1C) (OR 1.206, 95%CI 1.006 to 1.446, p<0.05) were associated to the incidence of new-onset hypertension in pre-hypertensive T2DM patients. Subgroup analysis found that for those overweight and blood glucose poor controlled pre-hypertensive T2DM patients, long-term PA were less likely to develop hypertension (overweight: OR 0.187, 95%CI 0.063 to 0.558, p<0.01; glucose poor controlled: OR 0.349, 95%CI 0.138 to 0.880, p<0.05).Conclusion These results suggested that long-term PA might be an important protective factor for new-onset hypertension in overweight and poor blood glucose controlled pre-hypertensive T2DM patients.