Objective To investigate the immunophenotype features of children with acute B-lymphoblastic leukemia(B-ALL) combined with fusion gene expressing after to analyze the results of the 43 fusion genes. Methods Real-time fluorescent probe PCR assay was used for the detection of fusion genes in 120 cases of children from Shenzhen Children's Hospital with B-ALL newly or recurrently diagnosed from Oct 2016 to Dec 2018. Multi-parameter flow cytometry(FCM) was used for the detection of the immunophenotype in children with B-ALL. Results Of all the 120 cases, the fusion genes were detected at positive rate of 37.5%(45/120), included TEL/AML1 27 cases, E2 A/PBX1 7 cases, BCR/ABL1 6 cases, MLL 4 cases, TLS/ERG 1 cases. The positive rate of leukemia fusion gene had statistically difference among fusion genes positive groups based on age(P<0.01). There was no statistically difference in the gender distribution(P>0.05). The expressing of CD19 was at positive rate of 100% in all of the groups. The rate of the common-B-ALL was the highest B-ALL subtype in the TEL/AML1 positive groups(77.8%). The stem /progenitor associated antigen CD34 was at positive rate of 81.5%. The pre-B-ALL was the main subtype in the E2 A/PBX1 group, which was no expression of the known T-ALL associated antigen MyAg antigen. There was statistically difference in the positive rate of MyAg expression among all of the groups(P<0.01), with the highest rate in the BCR/ABL1 group(100%). Conclusion There were certain distribution features in age composition and immunophenotype of children with B-ALL carrying five kinds of common fusion genes. The characteristic changes of the immunophenotype of B-ALL may be used to predict the expression of fusion genes and improve the accuracy of fusion genes by the supplementary role of immunophenotype analysis.