Background: This study aimed to investigate the correlation between the functional parameters of the left atrium (LA) derived from deformation imaging, two-dimensional (2D) speckle tracking echocardiography (STE), and tissue Doppler imaging (TDI) strain and strain rate (SR) and the function of the left atrial appendage (LAA) as measured by transesophageal echocardiography (TEE) in patients with primary valvular heart disease. Methods: This cross-sectional research included 200 primary valvular heart disease cases, categorized into Group I (n = 74) with thrombus and Group II (n = 126) without thrombus. All patients were subjected to standard 12 lead electrocardiography, transthoracic echocardiography (TTE), strain and SR imaging of the LA by TDI and 2D speckle tracking, and TEE. Results: At a cut-off value of <10.50%, peak atrial longitudinal strain (PALS) is a predictor of thrombus with an area under the curve (AUC) of 0.975 (95% CI: 0.957-0.993), sensitivity of 94.6%, specificity of 93.7%, positive predictive value (PPV) of 89.7%, negative predictive value (NPV) of 96.7%, and accuracy of 94%. At a cut-off value of <0.295 m/s, LAA emptying velocity is a predictor of thrombus with an AUC of 0.967 (95% CI: 0.944-0.989), sensitivity of 94.6%, specificity of 90.5%, PPV of 85.4%, NPV of 96.6%, and accuracy of 92%. The PALS (<10.50%) and LAA velocity (<0.295 m/s) are significant predictors of thrombus (P = 0.001, β = 2.745, SE = 0.804, OR = 15.56, and 95% CI: 3.219-75.245; and P = 0.002, β = 2.499, SE = 0.799, OR = 12.17, and 95% CI: 2.543-58.201, respectively). Peak systolic strain < 12.55% and SR < 1.065/s are insignificant predictors of thrombus (β = 1.167, SE = 0.996, OR = 3.21, and 95% CI: 0.456-22.631; and β = 1.443, SE = 0.929, OR = 4.23, and 95% CI: 0.685-26.141, respectively). Conclusions: Among LA deformation parameters derived from TTE, PALS is the best predictor of reduced LAA emptying velocity and LAA thrombus in primary valvular heart disease, regardless of the rhythm.