Background: Carotid intima-media thickness (cIMT), non-invasive marker of subclinical atherosclerosis, has been linked to future cardiovascular events, but its relationship with early cardiac remodeling and its shared genetic basis with cardiovascular disease (CVD) are not well defined. We investigated phenotypic and genetic associations between cIMT, aortic and cardiac imaging traits, and CVD in the UK Biobank. A total of 51,818 participants with carotid ultrasound and cardiac magnetic resonance imaging were included, excluding those with prior heart failure (HF), atrial fibrillation (AF), myocardial infarction, or stroke. Multivariable regression models examined associations between cIMT, aortic and cardiac traits, and CVD outcomes. Genetic correlations were estimated using linkage disequilibrium score regression, and gene-level and pathway analyses identified shared molecular mechanisms. Higher cIMT was significantly associated with larger ascending and descending aortic diameters, increased left ventricular (LV) mass, wall thickness, greater atrial and ventricular volumes, and reduced atrial ejection fractions (all P < 0.001). Elevated cIMT was associated with greater AF risk, and left cIMT additionally predicted HF independent of conventional risk factors. Genetically, cIMT showed positive correlations with descending aortic size, LV wall thickness, cardiac chamber volumes and mass, and a negative correlation with left atrial ejection fraction. Seven shared genes were identified, enriched in pathways related to extracellular matrix organization, vascular development and cardiac morphogenesis. Elevated cIMT is independently associated with systemic aortic and cardiac remodeling and impaired atrial function. Integrative genetic analyses highlight shared heritable mechanisms linking vascular thickening with myocardial remodeling, supporting cIMT as an early marker of cardiovascular structural change.