Studies on the association between pneumoconiosis and deep-vein thrombosis (DVT) and pulmonary thromboembolism (PE) are few. This study was based on data obtained from the Taiwan National Health Insurance Database from 2000 to 2006, with a follow-up period extending to the end of 2011. We identified 3719 pneumoconiosis patients and 14876 non-pneumoconiosis patients who were selected by frequency matched based on sex, age, and the index year. We analysed the risks of DVT and PE by using Cox proportional hazards regression models by including sex, age, and CCI score. The risk of developing PE was 1.90-fold in the patients with pneumoconiosis compared with the comparison cohort after adjustments for age, sex, and CCI score. By contrast, we did not observe significant effect of pneumoconiosis on DVT. However, the cumulative incidence curves for DVT were similar in the pneumoconiosis patients and non-pneumoconiosis patients. The multiplicative increased risks of PE were significant in patients with pneumoconiosis and CCI score of one and more. In conclusion, physicians should include pneumoconiosis in evaluating pulmonary embolism risk.