This study evaluates the prognostic significance of quantitative chimerism to monitor minimal residual disease and predict relapse in acute leukemia (AL) patients following allogeneic hematopoietic SCT (HSCT). The quantitative chimerism levels of 129 AL patients were measured using RQ-PCR based on 29 sequence polymorphisms. Receiver-operating characteristic curve indicated that the optimal cutoff point to predict an inevitable relapse was 1.0%, which results in 100.0% sensitivity and 79.6% specificity. The relapse rate of patients with chimerism> 1.0% at 2 years was 55.0%, whereas that for patients with chimerism< 1.0% was 0%(P= 0.000). Quantitative chimerism> 1.00% indicated a higher probability of relapse. Cox multivariate analysis indicated that quantitative chimerism> 1.00% was associated with lower disease-free survival (hazard ratio (HR)= 10.825; 95% confidence interval (CI)= 4.704–24.912, P= 0.000) and lower OS (HR= 8.681; 95% CI= 3.728–20.212, P= 0.000). Patients (24/47 with quantitative chimerism> 1.00%) who received preemptive modified DLI immunotherapy had significantly lower relapse rate (37.5%) than those (n= 9) who did not (100%; P= 0.001). Thus, quantitative chimerism is an independent prognostic factor that predicts clinical outcomes after HSCT and provides a guide for suitable interventions.