Mature B-cell acute lymphocytic leukaemia (B-ALL) is distinguished from B-cell non-Hodgkin lymphoma (B-NHL) by the arbitrariness of the 25% cut-off, and given that the percentage of bone marrow (BM) blasts can vary according to site of aspirate, we refrained from differentiating mature B-ALL from B-NHL with BM infiltration. A total of 156 patients from the Chinese Children Cancer Group with BM blasts of more than 5% and consistent with immunophenotypic features of mature B cells were included in this study. The 2-year progression-free survival, 2-year event-free survival and 2-year overall survival were 76.6 ± 3.6%, 69.7 ± 3.7% and 80.1 ± 3.3% respectively. Central nervous system (CNS) involvement, serum ferritin levels higher than four times normal and rituximab no more than two doses were associated with lower PFS. Male, bulky disease and head/neck region involvement were associated with higher rate of CNS invasion. We performed an integrative transcriptomic characterization of 36 cases. Structure variant included IG::MYC, IGH::CACS11, MEF2D::BCL9, IGH::VPS53 and ACIN1::NUTM1. SNV analysis uncovered driver variations affecting 10 recurrently mutated genes including ID3, TP53, MYC, ARID1A, SMARCA4, DDX3X, CCND3, RHOA, SMARCB1, FOXO1 and GNA13. Mature B-ALL/B-NHL with BM involvement was a heterogeneous group of malignancies in both clinical features and genetic alternations. Genetics analysis was helpful for making accurate diagnoses and guiding appropriate therapeutic strategies.