Hemodialysis patients are a special group of patients with higher mortality rates. Hemodialysis patients with vitamin D deficiency {plasma levels of 25-hydroxyvitamin D [25(OH)D] below 20 ng/mL} are associated with even higher mortality rates. The prognostic importance of vitamin D deficiency in hemodialysis patients with different cardiothoracic ratios (CTRs) is still unclear. This prospective study was performed in a single hemodialysis center, and 186 patients were included. This study analyzed the prognostic importance of vitamin D deficiency in hemodialysis patients with different CTRs. Vitamin D deficiency patients had a significantly higher prevalence of stroke and diabetic mellitus than those without vitamin D deficiency. In addition, the CTR was higher in patients with vitamin D deficiency than in those without vitamin D deficiency. After multivariate logistic regression, we found that CTR was the solitary factor that was independently significantly associated with vitamin D deficiency [odds ratio: 1.07, 95% confidence internal (CI): 1.01-1.13, p = 0.02]. Additionally, vitamin D deficiency was associated with all-cause mortality in patients with higher CTR after adjustment in hierarchical regression models. In conclusion, we reported that vitamin D deficiency was independently significantly associated with a higher CTR. We additionally revealed that vitamin D deficiency was an independent predicator for all-cause mortality in higher CTR hemodialysis patients.