AimsMechanical function of the left atrium (LA) and the left ventricle (LV) has been demonstrated to be a prognostic factor in patients with hypertrophic cardiomyopathy (HCM). We explore whether myocardial mechanical function can be improved by septal reduction therapy in symptomatic obstructive HCM.Methods and resultsAmong 65 patients who underwent septal myectomy for symptomatic obstructive HCM from 2006 to 2022, 44 were analysed after excluding those who underwent simultaneous valve repair or replacement or maze operation. LA and LV functional variables including LA strain and LV global longitudinal strain were evaluated by two‐dimensional and speckle‐tracking echocardiography and compared before and 1 year after surgery. After septal myectomy, LA volume index (58.1 ± 18.3 vs. 45.3 ± 14.6 mL/m2, P = 0.001) decreased significantly. As LV end‐systolic dimension increased after surgery, the LV ejection fraction decreased (73.8 ± 6.7 vs. 62.9 ± 8.3%, P < 0.001). LA strain (24.4 ± 9.3 vs. 30.5 ± 13.6%, P = 0.004) improved after septal myectomy, but LV global longitudinal strain deteriorated (−12.6 ± 3.6 vs. −11.6 ± 4.3%, P = 0.033), mainly related to worsening non‐septal longitudinal strain (−14.4 ± 4.3 vs. −10.9 ± 8.4%, P = 0.005).ConclusionsAs haemodynamic loads due to LV outflow tract obstruction was relieved through surgical septal reduction therapy in patients with symptomatic obstructive HCM, there was a significant reduction in LA volume and restoration of LA mechanical dysfunction. However, LV mechanical dysfunction deteriorated even after surgical septal reduction therapy.