This study was aimed to explore prognostic significance of minimal residual disease (MRD) detection in patients with acute myeloid leukemia (AML) by multiparameter flow cytometry (MCF). Leukemia-associated immunophenotype (LAIP) of newly diagnosed AML patients were determined by 4-color 5 antibody panels and patients with sensitive LAIP were chosen for MRD detection. 601 bone marrow samples from 95 patients were acquired after treatment and MRD were considered positive by the critical normal value plus twice standard deviation in normal bone marrow specimen. The patients were divided into three groups and the clinical significance was analyzed every 2 months within initial 6 months after induction treatment. The results showed that the relapse rate and relapse-free survival (RFS) rate were all significantly different between MRD positive and MRD negative patients in the three groups (p < 0.05). Patients with MRD positive had a median relapse-free survival time of 11 months, 11.5 months and 11 months at 1 - 2, 3 - 4 and 5 - 6 months respectively, while all patients with MRD negative were not observed to reach median release-free survival time (p < 0.05). Furthermore, the clinical significance was analyzed after induction and one course of consolidate treatment, the relapse rate of MRD positive and MRD negative patients were 57.14% versus 0% and 91.67% versus 2.27% respectively (p = 0.000 and p = 0.000). It is concluded that MRD detection by multi-parameter flow cytometry can predict outcome of AML patients, which should be continuously monitored after treatment.