The intricate relationship between atrial fibrillation (AF), blood flow disturbances, and thrombus emergence is well-established in humans. Thrombi primarily form in the left atrial appendage (LAA), but the specific role of LAA morphology in this process remains unclear. Felines, despite rarely experiencing AF, present a valuable model for studying human heart diseases. Cats exhibit a high incidence of cardiomyopathies, often accompanied by significant left atrial dilation and thrombus formation. This unique aspect prompts research into LAA morphology and function in thrombus development. Our study, using advanced image processing and fluid simulations on 24 cat hearts ranging from normal to cardiomyopathic subjects, aims to discern distinctions in left atrium (LA) and LAA morphologies, blood flow patterns, and their relation to thrombus formation. Significantly different variables in distinguishing groups include heart weight, LAA volume, LA volume, ostium area, ostium area-to-heart weight ratio, centreline length, and velocity at the ostium. Fluid simulations revealed lower LAA blood flow velocities and increased thrombotic risk in cases with thrombi. This study enhances our understanding of LAA structure and function, offering insights into thrombus formation mechanisms with potential implications for managing thrombosis risk in patients.