Nucleostemin (NS) plays an important role in tumorigenesis and progression. Most studies consider that NS plays its role through combining with p53 and inhibiting it, however our previous studies revealed that NS could also function without the existence of p53. To date, few studies have focused on the p53-independent pathway of NS, and its molecular mechanism remains unknown. The aim of the present study was to investigate the p53-independent pathway of NS in the human acute myeloid leukemia cell line HL-60 which was p53-null by using the DNA microarray technique. Lentivirus-mediated RNA interference technique was used to knock down NS expression in HL-60 cells, and then DNA microarray and bioinformatics were used to analyze the gene expression profiling changes. The microarray data showed that after knocking down NS in HL-60 cells, 2,628 differentially expressed genes were identified through ≥ 2 or ≤ 0.5-fold-change, in which 818 genes were upregulated and 1,810 genes were downregulated. Real-time quantitative polymerase chain reaction (qPCR) validated the reliability of DNA microarray data. Pathway analysis showed extensive signal pathways in HL-60 cells were influenced by inhibiting NS expression. In particular, the inhibition of PI3K-AKT pathway, JAK-STAT pathway, RAS-RAF-MEK-ERK1/2 pathway and activation of JNK pathway, p38 MAPK pathway may associate with the apoptosis of HL-60 cells after knocking down NS. The findings of this study provide insight to further explore the specific molecular mechanism of NS function in p53-null leukemia and they also lay the foundations for exploring new therapeutic targets for p53-null leukemia and even p53-null tumors.