Background Oral anticoagulants (OACs) are effective for the prophylaxis of stroke in patients with atrial fibrillation (AF). This cross-sectional study aimed to investigate the status of anticoagulation treatment for hospitalized AF patients in Southwest China. Methods A total of 4760 hospitalized patients with AF were enrolled from 21 hospitals in Chongqing city from January 1 to December 31, 2013. Results Among the enrolled patients, 3785 were diagnosed with nonvalvular AF. These patients had a mean age of 74.4±10.1 years. The mean CHADS 2 score of all subjects was 2.60±1.34, and 80.7% of the patients had CHADS 2 ≥2. The use rate of OACs was only 11.5% for patients with a high risk for stroke (CHADS 2 ≥2) and was much lower in patients from the second-level hospitals than in patients from the third-level hospitals (5.8% vs. 16.9%, P <0.001). The leading reason for the underuse of OACs in high-risk patients was physician’s nonfeasance. Conclusion This study demonstrated that the underuse of anticoagulation therapy in hospitalized patients with nonvalvular AF was particularly serious in Southwest China, especially in the second-level hospitals. Urgent and effective measures are desperately needed to improve this alarming situation in China.