Patients with end-stage renal disease have a high prevalence of cardiovascular disease. Chest radiography can be used to assess cardiothoracic ratio (CTR) and aortic arch calcification (AoAC). The aims of this longitudinal follow-up study were to investigate factors associated with changes in CTR and AoAC and understand whether these changes are associated with overall and cardiovascular mortality in hemodialysis (HD) patients. We enrolled 260 patients undergoing HD who had at least two available chest X-rays from 2008 to 2015. CTR and AoAC were assessed in each patient using measurements from baseline and annual chest X-rays. The CTR increased from 49.05% to 51.86% and the AoAC score increased from 3.84 to 9.73 over 7 years. The estimated slopes were 0.24 (p < 0.0001) for CTR and 0.08 (p = 0.0441) for AoAC. Increased AoAC, older age, female sex, coronary artery disease, and decreased albumin were associated with an increase in CTR, and older age, cerebrovascular disease, decreased albumin, increased Kt/V, and the use of antiplatelet agents were associated with an increase in AoAC. During follow-up, 136 of the 260 (52.3%) patients died, of whom 72 died due to cardiovascular causes. The change in CTR was greater in those who died (p = 0.0125) than in those who survived. The AoAC score was also higher in those who died than in those who survived, although there was no significant difference in the change in AoAC between the two groups (p = 0.8035). CTR and AoAC increased significantly over time in the HD patients in this longitudinal follow-up study, and the change in CTR was greater in those who died than in those who survived. Chest radiography is a simple and useful tool to assess the progression of CTR and AoAC as a prognostic marker.