Objective To investigate the molecular mechanism of inositol polyphosphate 5-phosphtase IV (INPP5E) gene on embryonic neural tube closure in mice. Methods All NTD embryos were examined carefully using a dissecting microscope. The structure changes of neural tube tissues were detected by HE stain, the crownrump length and body weight of embryos were measured. Bisulphite sequencing (BS) was used to detect the DNA methylation level within the promoter region of INPP5E in embryonic neural tissues of NTD and control group on embryonic day 11.5 (E 11.5). Real-time quantitative polymerase chain reaction (RT-PCR) and western blot was used to detect the transcription and expression levels of the INPP5E gene in neural tube tissues on E 11.5. UPLC-MS/ MS was used to detect the level of folic acid (FA), 5-methyltetrahydrofolate (5-MeTHF), 5-formyltetrahydrofolate (5-FoTHF) and homocysteine (Hcy) in embryonic neural tissues. Results Compared with control group, the methylation level of INPP5E promoter region in embryonic neural tissues were lower in NTD group on E 11.5 (P < 0.05), and the transcription level and the expression level of INPP5E were decreased (P < 0.05). Meanwhile, the concentrations of FA (2.76±0.98 VS 4.39±1.41 mg/g) and Hcy (4.33±1.42 VS 7.06±1.38 mg/g) increased (P < 0.05), and the concentrations of 5-MeTHF (9.55±2.38 VS 4.62±1.98 mg/g) and 5-FoTHF (4.86±1.02 VS 3.19±0.75 mg/g) decreased in embryonic neural tissues in the NTD group compared with the control group (P < 0.05). Conclusions The INPP5E gene plays an important role in regulation of embryonic neural closure. Reduced methylation level in INPP5E promoter region caused by folic acid metabolic disorder may be involved in the etiology of NTD by affecting its expression.