Objective To investigate the predictive value of deep learning-based cardiac ultrasound flow imaging for hypertrophic cardiomyopathy (HCM) complicated by arrhythmias. Methods The clinical data of 158 patients with hypertrophic cardiomyopathy were retrospectively collected from July 2019 to December 2021, and additionally divided into training group 106 cases, validation group 26 cases and test group 26 cases according to the ratio of 4:1:1, and divided into concurrent and non-concurrent groups according to whether they were complicated by arrhythmia or not, respectively. General data of patients (age, gender, BMI, systolic blood pressure, diastolic blood pressure, HR) were collected, a deep learning model for cardiac ultrasound flow imaging was established, and image data, LVEF, LAVI, E/e', vortex area change rate, circulation intensity change rate, mean blood flow velocity, and mean EL value were extracted. Results The differences in general data (age, gender, BMI, systolic blood pressure, diastolic blood pressure, HR) between the three groups were not statistically significant, P > 0.05. The differences in age, gender, BMI, systolic blood pressure, diastolic blood pressure, HR between the patients in the concurrent and non-concurrent groups in the training group were not statistically significant, P > 0.05. Conclusions Deep learning-based cardiac ultrasound flow imaging can identify cardiac ultrasound images more accurately and has a high predictive value for arrhythmias complicating hypertrophic cardiomyopathy, and vortex area change rate, circulation intensity change rate, mean flow velocity, mean EL, LAVI, and E/e' are all risk factors for arrhythmias complicating hypertrophic cardiomyopathy.