Background Atrial functional mitral regurgitation (AFMR) arises from left atrial (LA) dilation, commonly associated with atrial fibrillation, and leads to progressive cardiac damage. This study evaluated the prognostic value of a novel echocardiographic cardiac damage classification system for patients with moderate or severe AFMR. Methods In a retrospective multicentre study, 1007 patients with AFMR were stratified into four groups based on echocardiographic findings: group 1, LA damage (dilation); group 2, left ventricular damage (reduced ejection fraction and/or dilation); group 3, right heart damage (tricuspid regurgitation and/or pulmonary hypertension); and group 4, combined left and right heart damage. The primary outcome was a composite of all-cause death, heart failure hospitalisations and mitral valve (MV) interventions over a median follow-up of 3.0 years. Results The cohort’s mean age was 78±10 years, with 56% female. Event rates for the primary outcome were progressively higher across groups 1–4 (31.0%, 38.0%, 46.3% and 57.2%, respectively; p<0.001). After multivariable adjustment, group 4 was associated with a significantly higher risk of the primary outcome compared with group 1 (HR 1.65, 95% CI 1.29 to 2.11, p<0.001). This classification consistently stratified risks for individual components of the composite endpoint, particularly in patients without MV intervention. Conclusions A cardiac damage classification system based on echocardiographic parameters provides prognostic insights in patients with AFMR, identifying subgroups at higher risk of adverse outcomes. Future studies are needed to validate its use in guiding therapeutic decisions.