We studied the effects of neutrons, neutrons and γ rays, and γ rays exposures on the transcription spectrum in human peripheral blood of three healthy adult men. Samples were irradiated with 1.42 Gy 2.5-MeV neutrons, 0.71 Gy neutrons and 0.71 Gy ¹³⁷Cs γ rays, and 1.42 Gy ¹³⁷Cs γ rays. Transcriptome sequencing identified 56 differentially co-expressed genes and enriched 26 KEGG pathways. There are 97, 45 and 30 differentially expressed genes in neutron, neutron and γ ray combined treatment, and γ rays, respectively, and 21, 3 and 8 KEGG pathways with significant differences are enriched. Fluorescence quantitative polymerase chain reaction (qPCR) verified differential co-expression of AEN, BAX, DDB2, FDXR, and MDM2. Additionally, irradiation of AHH-1 human lymphocytes with a ²⁵²Cf neutron source at 0, 0.14, 0.35, and 0.71 Gy, fluorescence qPCR revealed a dose-response relationship for BAX, DDB2, and FDXR at dose ranges of 0–0.71 Gy, with R² of 0.803, 0.999, and 0.999, respectively. Thus, neutrons can induce more differentially expressed genes and enrich more pathways. Combined treatment of neutrons and γ-rays may incorporate damage of both high and low LET, the genes activated by neutrons and γ rays combined are almost the combination of genes activated by neutron and γ rays combined treatment. BAX, DDB2 and FDXR are differentially expressed after irradiation by Deuterium-Deuterium (D-D) neutron source and ²⁵²Cf neutron source, so they are expected to be molecular targets of neutron damage.