Background Invasive fungal disease (IFD) is a severe complication after haploidentical stem cell transplantation (haplo-HSCT) and has a poor prognosis. It has been shown that genetic polymorphism may be one possible reason for the increased risk of IFD. This study aimed to assess the role of genetic polymorphisms in the level of susceptibility to IFD in after haplo-HSCT. Methods In this study, we prospectively enrolled 251 patients who received haplo-HSCT at the Peking University Institute of Hematology from to 2016-2018. Forty-three single nucleotide polymorphisms (SNPs) of the genomic DNA were genotyped in blood samples from both recipient and donor. Results Twenty-two patients (8.8%) were diagnosed with proven or probable IFD. The independent risk factors for IFD were grades 3-4 acute graft-versus-host disease, cytomegalovirus reactivation, and recipient and donor rs2305619 (PTX3) (P<0.05) in multivariate analysis. Meanwhile, we combined the variables to develop the IFD risk scoring system and stratified patients into low- (0), intermediate- (1-2), and high-risk (3-4) groups. The 30-day and 100-day cumulative incidence of IFD in the low-, intermediate-, and high-risk groups were 0.1%, 2.4%, 10.2% and 4.5%, 4.1%, 20.3%, respectively (P=0.015). Conclusions PTX3 rs2305619 polymorphisms increase the susceptibility of IFD after haplo-HSCT in the Chinese Han population, and the IFD scoring system could be considered as a new standard for risk stratification for IFD after HSCT.