Abstract: Objective To investigate the safety and efficacy of Caspofungin in secondary prevention of fungi in patients with allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods The clinical data of 40 cases of allo-HSCT with fungal infection stratified according to the 2010 edition of Diagnostic Standards and Therapeutic Principles for Invasive Fungal Infection in Patients with Hematological Diseases/Malignant Tumors (Revised edition) in our hospital from January 2013 to April 2017 were reviewed. All patients were administrated with Caspofungin. The stratified diagnosis of patients was analyzed, and the clinical efficacy and adverse reactions of Caspofungin were evaluated. Results After stratified diagnosis and treatment with Caspofungin, the effective rate in the 4 confirmed patients was 100.00%, in 22 clinically diagnosed patients was 77.27%, and in 14 prospectively diagnosed patients was 71.43%. There was no significant difference in the effective rate between clinically diagnosed patients and prospectively diagnosed patients (P>0.05). In the course of treatment, the main adverse reactions were hypokalemia (9 cases) and hypoglycemia (7 cases). After symptomatic treatment, the symptoms were alleviated. Conclusion Caspofungin has good therapeutic effect, with fewer adverse reactions and high safety in allogeneic hematopoietic stem cell transplantation. It is worth popularizing in secondary prevention of bacterial infection.