Objective To explore the value of three-dimensional speckle tracking echocardiography (3D-STE) combined with myocardial strain technique in evaluating the early myocardial functional injury in hypertrophic cardiomyopathy (HCM). Method Prospective cohort study, 120 patients with HCM who were admitted to Zhoukou Central Hospital from February 2023 to February 2026 were selected as the research subjects. All of them underwent 3D-STE combined with myocardial strain technique examination. The left ventricular systolic and diastolic functions were evaluated based on echocardiography (ECHO). The patients were divided into the occurrence group and the non-occurrence group according to whether they had myocardial function impairment. Results The incidence of early myocardial dysfunction in 120 HCM patients was 45.00% (54/120). The incidence of hypertension, atrial fibrillation, maximum left ventricular wall thickness (MLVWT), interventricular septal thickness (IVS), and early diastolic mitral flow velocity/early diastolic mitral annulus velocity (E/e’) in occurrence group were higher than those in the non-occurrence group (all P＜0.05), the global longitudinal strain (GLS), global circumferential strain (GCS) were also significantly higher. The in and GAS values were significantly lower than those in the non occurrence group (all P＜0.05). Multivariate Logistic regression showed that comorbidities of hypertension, atrial fibrillation, MLVWT, IVS, E/e’, GLS, GCS, and GAS were all influencing factors of early myocardial dysfunction in HCM patients (all P＜0.05). Receiver operator characteristic (ROC) curve showed that the area under the curve (AUC) of MLVWT, IVS, E/e’, GLS, GCS, and GAS alone and in combination for evaluating early myocardial functional injury in HCM patients were 0.758, 0.764, 0.756, 0.772, 0.774, 0.777, and 0.942, respectively, indicating a high value for combined evaluation. Conclusion The combination of 3D-STE and myocardial strain technology has certain evaluation value for early myocardial functional injury in HCM, and can provide reference for clinical prevention and treatment.