The purpose of this paper is to present the research on the molecular biological characteristics of proto-oncogene pim-2 and to analyze the related mechanism. Proto-oncogene pim-2 was studied and analyzed by the bioinformatics method and technology. With an online server, the chromosomal localization of pim-2 gene was analyzed, and the exon, open reading frame, CpG island and miRNAs complementary fragments and the like were predicted. With bioinformatics software, the physicochemical property of transcription protein of proto-oncogene pim-2 and various modification sites of protein sequence, such as ubiquitination and glycosylation, were predicted, the antigenic index was calculated, and the spatial structural was modeled. The research findings showed that the proto-oncogene pim-2 comprised six exons, the CDS (coding sequence) transcribed a section of peptide chain including 311 amino acids, a gene promoter has a CpG island, and the 3'UTR region contains an miRNA gene. The molecular weight of the Pim-2 protein was 34, 188.47, the isoelectric point was 5.78, the instability index was 45.87, and the extinction coefficient was 279nm. A plurality of covalent modification sites, two ubiquitination sites, four glycosylation sites, an SUMO sumoylation site, a nitrosation site, two palmitoylation sites and sixteen regions with higher antigenic index were distributed in the protein sequence. This research showed that the related regions and modification sites distributed on the sequence of proto-oncogene pim-2 were closely related to the carcinogenic effect thereof.